Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	TTotCov	TVarCov	NTotCov	NVarCov	TVarRat	NVarRat	dbSNP_AF	dbSNP_PopFreq	dbSNP_Strength	COSMIC_Codon	COSMIC_Gene	COSMIC_Gene_Freq	COSMIC_Site_Freq	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	Confidence	Algorithm
NUP214	8021	hgsc.bcm.edu	37	9	134073007	134073008	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	86.0	17.0	102.0	0.0	0.198	.	.	.	none	.	NUP214	166	.	NM_005085	exon29	c.4126_4127insC	p.A1376fs	.	.	PASS	Pindel,Atlas-Indel
CHD7	55636	hgsc.bcm.edu	37	8	61714117	61714118	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	164.0	28.0	138.0	0.0	0.171	.	.	.	none	.	CHD7	534	.	NM_017780	exon6	c.2407_2408insA	p.E803fs	.	.	PASS	Pindel,Atlas-Indel
RBM33	155435	hgsc.bcm.edu	37	7	155532534	155532545	+	In_Frame_Del	DEL	CCCACCCCAGCA	CCCACCCCAGCA	-	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	CCCACCCCAGCA	CCCACCCCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	25.0	13.0	41.0	0.0	0.52	0	.	.	none	.	RBM33	157	.	NM_053043	exon12	c.1862_1873del	p.621_625del	.	.	PASS	Atlas-Indel
PALM3	342979	hgsc.bcm.edu	37	19	14167553	14167553	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	108.0	39.0	117.0	0.0	0.361111	0	.	.	none	.	PALM3	26	.	NM_001145028	exon3	c.G190T	p.D64Y	TGGGGTCTTCGGA	.	PASS	Atlas-SNP
GRIA2	2891	hgsc.bcm.edu	37	4	158142838	158142838	+	Silent	SNP	C	C	T	rs371935251	alternate_allele	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	83.0	17.0	100.0	0.0	0.204819	0	.	.	alt	GRIA2_ENST00000264426,NS,carcinoma,0,2	GRIA2	358	2	NM_000826	exon2	c.C108T	p.G36G	TAGGGGCGCCGAT	.	PASS	Atlas-SNP
ITGB3	3690	hgsc.bcm.edu	37	17	45369814	45369814	+	Missense_Mutation	SNP	C	C	T	rs145572861	bycluster;byfrequency;by1000genomes	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	41.0	17.0	50.0	0.0	0.414634	0	C|1.000;T|0.000	0.000	strong	.	ITGB3	157	.	NM_000212	exon10	c.C1570T	p.R524W	AGCCAGCGGGGCG	.	PASS	Atlas-SNP
ETAA1	54465	hgsc.bcm.edu	37	2	67631813	67631813	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	100.0	42.0	99.0	0.0	0.42	0	.	.	none	.	ETAA1	88	.	NM_019002	exon5	c.G1999A	p.E667K	ATATGTGAGATCA	.	PASS	Atlas-SNP
TP53	7157	hgsc.bcm.edu	37	17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	rs121912651	bycluster	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	44.0	30.0	95.0	0.0	0.681818	0	.	.	weak	TP53_ENST00000545858,NS,adenocarcinoma,+1,1635	TP53	33396	1635	NM_000546	exon7	c.C742T	p.R248W	GCCTCCGGTTCAT	.	PASS	Atlas-SNP
NPEPL1	79716	hgsc.bcm.edu	37	20	57269610	57269610	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	71.0	31.0	84.0	0.0	0.43662	0	.	.	none	.	NPEPL1	36	.	NM_024663	exon3	c.G469A	p.G157R	CTGGTGGGACAAG	.	PASS	Atlas-SNP
DTX1	1840	hgsc.bcm.edu	37	12	113496201	113496201	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	32.0	11.0	31.0	0.0	0.34375	0	.	.	none	DTX1,NS,lymphoid_neoplasm,+1,1	DTX1	83	1	NM_004416	exon1	c.G204A	p.Q68Q	CGCCCAGCTTGTG	.	PASS	Atlas-SNP
STAT4	6775	hgsc.bcm.edu	37	2	191905872	191905872	+	Silent	SNP	G	G	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	158.0	32.0	171.0	0.0	0.202532	0	.	.	none	STAT4,rectum,carcinoma,0,1	STAT4	85	1	NM_001243835	exon15	c.C1254A	p.G418G	GTGACAGCCCTAA	.	PASS	Atlas-SNP
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18680514	18680514	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	45.0	16.0	50.0	0.0	0.355556	0	.	.	none	.	ADAMTSL1	306	.	NM_052866	exon11	c.G1341A	p.P447P	GTCTCCGGTAACT	.	PASS	Atlas-SNP
REPS1	85021	hgsc.bcm.edu	37	6	139262508	139262508	+	Silent	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	69.0	51.0	156.0	0.0	0.73913	0	.	.	none	.	REPS1	58	.	NM_001128617	exon8	c.T1099C	p.L367L	GCATTAAGCTTTC	.	PASS	Atlas-SNP
OR8K5	219453	hgsc.bcm.edu	37	11	55927085	55927085	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	143.0	16.0	96.0	0.0	0.111888	0	.	.	none	OR8K5,NS,carcinoma,0,2	OR8K5	82	2	NM_001004058	exon1	c.G709C	p.A237P	AGAAAGCCTTTTT	.	PASS	Atlas-SNP
PER1	5187	hgsc.bcm.edu	37	17	8053822	8053822	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	44.0	25.0	76.0	0.0	0.568182	0	.	.	none	.	PER1	104	.	NM_002616	exon2	c.G203A	p.R68Q	GAGCTCCGCTGAG	.	PASS	Atlas-SNP
BNC2	54796	hgsc.bcm.edu	37	9	16727796	16727796	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	99.0	45.0	152.0	0.0	0.454545	0	.	.	none	.	BNC2	166	.	NM_017637	exon3	c.A329T	p.Q110L	CTTACCTGTTGGG	.	PASS	Atlas-SNP
C1S	716	hgsc.bcm.edu	37	12	7172542	7172542	+	Missense_Mutation	SNP	G	G	A	rs147341600	bycluster	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	129.0	20.0	130.0	0.0	0.155039	0	G|1.000;A|0.000	0.000	weak	.	C1S	93	.	NM_201442	exon6	c.G656A	p.R219Q	CCTTGCGGAGAGA	.	PASS	Atlas-SNP
TAPT1	202018	hgsc.bcm.edu	37	4	16165144	16165144	+	Silent	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	177.0	43.0	203.0	0.0	0.242938	0	.	.	none	.	TAPT1	31	.	NM_153365	exon14	c.A1491G	p.E497E	CAGGTTTTCTTCT	.	PASS	Atlas-SNP
GPATCH4	54865	hgsc.bcm.edu	37	1	156565049	156565049	+	Missense_Mutation	SNP	A	A	C	rs77528517	bycluster;byfrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	280.0	14.0	333.0	0.0	0.05	0	A|0.333;C|0.333;G|0.333	0.333	strong	.	GPATCH4	34	.	NM_015590	exon8	c.T1084G	p.F362V	ACCTAAAAGTTTC	.	PASS	Atlas-SNP
FAM181B	220382	hgsc.bcm.edu	37	11	82444591	82444591	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	64.0	42.0	50.0	0.0	0.65625	0	.	.	none	.	FAM181B	14	.	NM_175885	exon1	c.G181A	p.E61K	TGGCCTCGCGCAC	.	PASS	Atlas-SNP
SRPR	6734	hgsc.bcm.edu	37	11	126134971	126134971	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	68.0	17.0	59.0	0.0	0.25	0	.	.	none	.	SRPR	60	.	NM_003139	exon11	c.C1408T	p.R470W	AACGCCGGGTGTG	.	PASS	Atlas-SNP
LMNB1	4001	hgsc.bcm.edu	37	5	126113530	126113530	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	24.0	10.0	37.0	0.0	0.416667	0	.	.	none	.	LMNB1	49	.	NM_005573	exon1	c.C330T	p.C110C	CAAGTGCAAGGCG	.	PASS	Atlas-SNP
SEC24B	10427	hgsc.bcm.edu	37	4	110384430	110384430	+	Silent	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	187.0	38.0	205.0	0.0	0.203209	0	.	.	none	.	SEC24B	186	.	NM_006323	exon2	c.T507C	p.S169S	CAGCTCTTCTGTT	.	PASS	Atlas-SNP
TRIM72	493829	hgsc.bcm.edu	37	16	31230671	31230671	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	62.0	11.0	99.0	0.0	0.177419	0	.	.	none	.	TRIM72	32	.	NM_001008274	exon4	c.T548C	p.L183P	TGTTCCTGGCTGC	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274827	203274827	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	66.0	13.0	85.0	0.0	0.19697	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.C93G	p.S31R	CGTGAGCGAGCAG	.	PASS	Atlas-SNP
LAMB1	3912	hgsc.bcm.edu	37	7	107603364	107603364	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	203.0	51.0	216.0	2.0	0.251232	0.00925926	.	.	none	LAMB1,NS,carcinoma,0,1	LAMB1	185	1	NM_002291	exon15	c.C1843T	p.R615C	CGTAGCGAATTAG	.	scavenged	Atlas-SNP
PCDHB5	26167	hgsc.bcm.edu	37	5	140517068	140517068	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	56.0	24.0	85.0	0.0	0.428571	0	.	.	none	PCDHB5,NS,carcinoma,+1,1	PCDHB5	184	1	NM_015669	exon1	c.G2052A	p.S684S	CGACTCGCTCACT	.	PASS	Atlas-SNP
ZNRF4	148066	hgsc.bcm.edu	37	19	5455866	5455866	+	Missense_Mutation	SNP	G	G	A	rs375118147		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	26.0	7.0	34.0	0.0	0.269231	0	.	.	weak	.	ZNRF4	59	.	NM_181710	exon1	c.G364A	p.V122I	TTCGGCGTCCCCC	.	PASS	Atlas-SNP
MAP1B	4131	hgsc.bcm.edu	37	5	71492363	71492363	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	36.0	14.0	50.0	0.0	0.388889	0	.	.	none	.	MAP1B	243	.	NM_005909	exon5	c.C3181A	p.Q1061K	GAGGAGCAGTATG	.	PASS	Atlas-SNP
CTSC	1075	hgsc.bcm.edu	37	11	88070757	88070757	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	194.0	23.0	165.0	0.0	0.118557	0	.	.	none	.	CTSC	46	.	NM_148170	exon1	c.C84T	p.A28A	GCAGTTGGCAGGT	.	PASS	Atlas-SNP
ABCG4	64137	hgsc.bcm.edu	37	11	119031694	119031694	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	164.0	41.0	138.0	0.0	0.25	0	.	.	none	.	ABCG4	77	.	NM_022169	exon15	c.C1819T	p.R607X	ATCCTCCGAGCGC	.	PASS	Atlas-SNP
GUF1	60558	hgsc.bcm.edu	37	4	44680787	44680787	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	242.0	37.0	278.0	0.0	0.152893	0	.	.	none	.	GUF1	72	.	NM_021927	exon1	c.A148G	p.S50G	CTCTACAGCTCCG	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33041313	33041313	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	49.0	18.0	75.0	0.0	0.367347	0	.	.	none	.	HLA-DPA1	20	.	NM_033554	exon1	c.C35G	p.A12G	ATCACAGCTCTGA	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	37	12	85459141	85459141	+	Silent	SNP	T	T	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	96.0	28.0	118.0	0.0	0.291667	0	.	.	none	.	LRRIQ1	512	.	NM_001079910	exon9	c.T2493G	p.T831T	ATTAACTTCTTTG	.	PASS	Atlas-SNP
DTX1	1840	hgsc.bcm.edu	37	12	113496024	113496024	+	Silent	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	71.0	26.0	101.0	0.0	0.366197	0	.	.	none	.	DTX1	83	.	NM_004416	exon1	c.G27C	p.L9L	TGGGCTGATGCCT	.	PASS	Atlas-SNP
GBX2	2637	hgsc.bcm.edu	37	2	237076128	237076128	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	38.0	18.0	69.0	0.0	0.473684	0	.	.	none	.	GBX2	20	.	NM_001485	exon1	c.G487A	p.A163T	AGAAGGCGAGCAG	.	PASS	Atlas-SNP
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056330	26056330	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	180.0	38.0	183.0	0.0	0.211111	0	.	.	none	HIST1H1C,colon,carcinoma,0,2	HIST1H1C	80	2	NM_005319	exon1	c.G327C	p.K109N	TGCCTTCTTGTTG	.	PASS	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84609323	84609323	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	77.0	43.0	74.0	0.0	0.558442	0	.	.	none	.	.	.	.	NM_001001670	exon4	c.C3938T	p.T1313I	TGGGGACATCCCA	.	PASS	Atlas-SNP
OR51I2	390064	hgsc.bcm.edu	37	11	5475352	5475352	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	338.0	51.0	359.0	0.0	0.150888	0	.	.	none	.	OR51I2	76	.	NM_001004754	exon1	c.T634C	p.F212L	GACCTGTTTTTTA	.	PASS	Atlas-SNP
STAT3	6774	hgsc.bcm.edu	37	17	40475063	40475063	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	76.0	25.0	87.0	0.0	0.328947	0	.	.	none	STAT3,NS,lymphoid_neoplasm,-1,1	STAT3	268	1	NM_003150	exon20	c.A1847G	p.E616G	CCTCCTTCTTTGC	.	PASS	Atlas-SNP
GCNT1	2650	hgsc.bcm.edu	37	9	79118237	79118237	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	116.0	53.0	120.0	0.0	0.456897	0	.	.	none	.	GCNT1	52	.	NM_001490	exon4	c.G940A	p.D314N	GCACAAGACACAT	.	PASS	Atlas-SNP
BCL11A	53335	hgsc.bcm.edu	37	2	60688036	60688036	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	68.0	7.0	59.0	0.0	0.102941	0	.	.	none	.	BCL11A	298	.	NM_018014	exon4	c.G2011A	p.D671N	AGGGATCTTTGAG	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539203	92539203	+	Silent	SNP	G	G	A	rs369374957	alternate_allele	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	141.0	65.0	161.0	0.0	0.460993	0	.	.	alt	BTG1,NS,lymphoid_neoplasm,0,3	BTG1	30	3	NM_001731	exon1	c.C109T	p.L37L	TCTGCAGCTGTCG	.	PASS	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120631489	120631489	+	Silent	SNP	A	A	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	120.0	53.0	137.0	0.0	0.441667	0	.	.	none	.	ENPP2	254	.	NM_001130863	exon5	c.T474A	p.P158P	CCCTGCAGGGCAT	.	PASS	Atlas-SNP
MCOLN1	57192	hgsc.bcm.edu	37	19	7593558	7593558	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	118.0	52.0	153.0	0.0	0.440678	0	.	.	none	MCOLN1,colon,carcinoma,+1,1	MCOLN1	54	1	NM_020533	exon8	c.G953A	p.R318H	GCGCCCGCTCACT	.	PASS	Atlas-SNP
MAP1S	55201	hgsc.bcm.edu	37	19	17838807	17838807	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	68.0	20.0	89.0	0.0	0.294118	0	.	.	none	.	MAP1S	74	.	NM_018174	exon5	c.C2614T	p.R872C	AACTCACGCGCTG	.	PASS	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	37	19	19651184	19651184	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	35.0	15.0	56.0	0.0	0.428571	0	.	.	none	.	CILP2	84	.	NM_153221	exon3	c.G335A	p.R112H	GCGAGCGCGTGCA	.	PASS	Atlas-SNP
NPEPL1	79716	hgsc.bcm.edu	37	20	57269609	57269609	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	72.0	31.0	84.0	0.0	0.430556	0	.	.	none	.	NPEPL1	36	.	NM_024663	exon3	c.G468A	p.V156V	CCTGGTGGGACAA	.	PASS	Atlas-SNP
SHANK2	22941	hgsc.bcm.edu	37	11	70505972	70505972	+	Silent	SNP	C	C	T	rs141960453		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	139.0	83.0	113.0	0.0	0.597122	0	C|1.000;T|0.000	0.000	weak	.	SHANK2	340	.	NM_133266	exon2	c.G258A	p.A86A	TTGCCACGCCACC	.	PASS	Atlas-SNP
CD79B	974	hgsc.bcm.edu	37	17	62006798	62006798	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	51.0	40.0	84.0	1.0	0.784314	0.0119048	.	.	none	CD79B,NS,lymphoid_neoplasm,-1,13	CD79B	38	13	NM_001039933	exon5	c.A590T	p.Y197F	ACCTCGTAGGTGT	.	scavenged	Atlas-SNP
KCND2	3751	hgsc.bcm.edu	37	7	119915438	119915438	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	183.0	27.0	127.0	0.0	0.147541	0	.	.	none	.	KCND2	194	.	NM_012281	exon1	c.C752T	p.A251V	CTGCAGCGCCTAG	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37139203	37139203	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	64.0	10.0	71.0	0.0	0.15625	0	.	.	none	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	NM_001243186	exon4	c.G816C	p.E272D	CGGCGAGCTCAAG	.	PASS	Atlas-SNP
SDK2	54549	hgsc.bcm.edu	37	17	71434182	71434182	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	48.0	20.0	80.0	0.0	0.416667	0	.	.	none	.	SDK2	219	.	NM_001144952	exon7	c.C837T	p.A279A	GTAGCCGGCGTCA	.	PASS	Atlas-SNP
IZUMO3	100129669	hgsc.bcm.edu	37	9	24545061	24545061	+	Splice_Site	SNP	T	T	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	170.0	68.0	217.0	0.0	0.4	0	.	.	none	.	.	.	.	NM_001271706	exon4	c.302-2A>C	.	GACACCTAAGAGG	.	PASS	Atlas-SNP
CGN	57530	hgsc.bcm.edu	37	1	151508789	151508789	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	179.0	37.0	215.0	0.0	0.206704	0	.	.	none	.	CGN	106	.	NM_020770	exon19	c.G3274A	p.E1092K	GAAGACGAGCGGC	.	PASS	Atlas-SNP
MYD88	4615	hgsc.bcm.edu	37	3	38182641	38182641	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	92.0	76.0	62.0	0.0	0.826087	0	.	.	none	MYD88,NS,lymphoid_neoplasm,0,828	MYD88	900	828	NM_001172569	exon4	c.T613C	p.X205R	AGCGACTGATCCC	.	PASS	Atlas-SNP
RFX5	5993	hgsc.bcm.edu	37	1	151318690	151318690	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	89.0	16.0	98.0	0.0	0.179775	0	.	.	none	.	RFX5	69	.	NM_000449	exon3	c.G107A	p.G36D	ATGGTACCTCGGA	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62256044	62256044	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	149.0	127.0	207.0	0.0	0.852349	0	.	.	none	.	VPS13C	506	.	NM_020821	exon32	c.C3321G	p.I1107M	AATCTTGATTTCG	.	PASS	Atlas-SNP
ITPKB	3707	hgsc.bcm.edu	37	1	226925103	226925103	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	39.0	13.0	57.0	0.0	0.333333	0	.	.	none	ITPKB_ENST00000429204,scalp,carcinoma,-2,1	ITPKB	158	1	NM_002221	exon2	c.G57A	p.E19E	CTTCATCTCGTTG	.	PASS	Atlas-SNP
FAM189B	10712	hgsc.bcm.edu	37	1	155220451	155220451	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	37.0	18.0	63.0	0.0	0.486486	0	.	.	none	.	FAM189B	51	.	NM_006589	exon9	c.C1126T	p.L376F	GGCTGAGGCAGTA	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37139086	37139086	+	Missense_Mutation	SNP	G	G	C	rs33989191	bycluster;byfrequency;by1000genomes	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	80.0	14.0	114.0	0.0	0.175	0	G|0.998;C|0.002	0.002	strong	.	PIM1	71	.	NM_001243186	exon4	c.G699C	p.E233D	AGAGGAGCTGGCC	.	PASS	Atlas-SNP
C2orf71	388939	hgsc.bcm.edu	37	2	29296353	29296353	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	53.0	8.0	89.0	0.0	0.150943	0	.	.	none	.	C2orf71	146	.	NM_001029883	exon1	c.G775A	p.E259K	GGGGCTCTCTTTT	.	PASS	Atlas-SNP
PUS1	80324	hgsc.bcm.edu	37	12	132426407	132426407	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	89.0	37.0	103.0	0.0	0.41573	0	.	.	none	.	PUS1	47	.	NM_025215	exon5	c.A1115G	p.H372R	AGGAGCACATCTA	.	PASS	Atlas-SNP
AKAP4	8852	hgsc.bcm.edu	37	X	49957130	49957130	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	133.0	97.0	204.0	0.0	0.729323	0	.	.	none	.	AKAP4	131	.	NM_003886	exon5	c.G2234C	p.G745A	ATTGCACCACTGT	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186007087	186007087	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	88.0	16.0	118.0	0.0	0.181818	0	.	.	none	.	HMCN1	797	.	NM_031935	exon37	c.C5771G	p.A1924G	AAGATGCTGGAAA	.	PASS	Atlas-SNP
SOX7	83595	hgsc.bcm.edu	37	8	10587841	10587841	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	84.0	31.0	110.0	0.0	0.369048	0	.	.	none	.	SOX7	50	.	NM_031439	exon1	c.C103T	p.P35S	CCGGGGGCCGGGG	.	PASS	Atlas-SNP
NAV3	89795	hgsc.bcm.edu	37	12	78400358	78400358	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	89.0	16.0	99.0	0.0	0.179775	0	.	.	none	.	NAV3	506	.	NM_014903	exon8	c.T1040A	p.M347K	CCACCATGTTGAC	.	PASS	Atlas-SNP
SON	6651	hgsc.bcm.edu	37	21	34922547	34922547	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	67.0	21.0	70.0	0.0	0.313433	0	.	.	none	.	SON	343	.	NM_032195	exon3	c.T1010C	p.L337P	AAGCGCTAAGATT	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138563	37138563	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	73.0	15.0	52.0	0.0	0.205479	0	.	.	none	.	PIM1	71	.	NM_001243186	exon2	c.C370A	p.P124T	AAGGAGCCCCTGG	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138402	37138402	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	60.0	16.0	89.0	0.0	0.266667	0	.	.	none	.	PIM1	71	.	NM_001243186	exon1	c.C324T	p.C108C	GCCCTGCAACGAC	.	PASS	Atlas-SNP
KIRREL3	84623	hgsc.bcm.edu	37	11	126299147	126299147	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	108.0	19.0	110.0	0.0	0.175926	0	.	.	none	.	KIRREL3	183	.	NM_032531	exon15	c.G1733A	p.R578Q	TCCACTCGGATAT	.	PASS	Atlas-SNP
LGALS13	29124	hgsc.bcm.edu	37	19	40095831	40095831	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	78.0	19.0	94.0	0.0	0.24359	0	.	.	none	.	LGALS13	22	.	NM_013268	exon3	c.C106A	p.L36M	CCACAGCTGCAGG	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51523890	51523890	+	Silent	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	88.0	15.0	84.0	0.0	0.170455	0	.	.	none	.	PKHD1	927	.	NM_138694	exon61	c.T11034C	p.I3678I	GGATGAAATCATT	.	PASS	Atlas-SNP
HIST2H2BE	8349	hgsc.bcm.edu	37	1	149857872	149857872	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	116.0	51.0	125.0	0.0	0.439655	0	.	.	none	.	HIST2H2BE	33	.	NM_003528	exon1	c.C319G	p.L107V	TGGCCAGCTCGCC	.	PASS	Atlas-SNP
TEX13A	56157	hgsc.bcm.edu	37	X	104464743	104464743	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	60.0	25.0	110.0	0.0	0.416667	0	.	.	none	.	TEX13A	55	.	NM_031274	exon2	c.G339A	p.K113K	CCTGAGCTTCTTC	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891217	44891217	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	68.0	3.0	79.0	0.0	0.0441176	0	.	.	none	ZNF285,NS,carcinoma,0,2	ZNF285	86	2	NM_152354	exon4	c.A1190G	p.E397G	GGCTTCTCTCCAG	.	scavenged	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101730000	101730000	+	Splice_Site	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	334.0	117.0	385.0	1.0	0.350299	0.0025974	.	.	none	.	PABPC1	76	.	NM_002568	exon4	c.503+1G>T	.	AACTTACACTTTG	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77401400	77401400	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	127.0	63.0	126.0	0.0	0.496063	0	.	.	none	.	ADAMTS18	270	.	NM_199355	exon4	c.G716A	p.R239Q	GTCTCTCGACTCT	.	PASS	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112419851	112419851	+	Missense_Mutation	SNP	C	C	T	rs373730711		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	94.0	30.0	142.0	0.0	0.319149	0	.	.	weak	.	MCC	234	.	NM_001085377	exon10	c.G1582A	p.E528K	ACGATTCGGACCT	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274831	203274831	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	66.0	41.0	84.0	0.0	0.621212	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.C97A	p.Q33K	AGCGAGCAGAGGC	.	PASS	Atlas-SNP
BMPER	168667	hgsc.bcm.edu	37	7	33945290	33945290	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	83.0	15.0	79.0	0.0	0.180723	0	.	.	none	BMPER,NS,carcinoma,-1,1	BMPER	131	1	NM_133468	exon2	c.C65T	p.T22M	GGATTACGTGCTG	.	PASS	Atlas-SNP
DTX1	1840	hgsc.bcm.edu	37	12	113496139	113496139	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	61.0	19.0	79.0	0.0	0.311475	0	.	.	none	.	DTX1	83	.	NM_004416	exon1	c.A142T	p.I48F	CACCACATTGAGA	.	PASS	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156969	26156969	+	Silent	SNP	G	G	A	rs376044340		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	88.0	23.0	96.0	0.0	0.261364	0	.	.	weak	.	HIST1H1E	69	.	NM_005321	exon1	c.G351A	p.K117K	AGCCAAGCCTAAG	.	PASS	Atlas-SNP
ERBB4	2066	hgsc.bcm.edu	37	2	212587162	212587162	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	128.0	21.0	165.0	0.0	0.164062	0	.	.	none	.	ERBB4	480	.	NM_001042599	exon7	c.A839C	p.N280T	TTTGCATTGAAAT	.	PASS	Atlas-SNP
UBE2A	7319	hgsc.bcm.edu	37	X	118717088	118717088	+	Splice_Site	SNP	A	A	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	42.0	34.0	71.0	0.0	0.809524	0	.	.	none	.	UBE2A	43	.	NM_181762	exon5	c.241-2A>C	.	CTCTTTAGTCTCT	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170060578	170060578	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	151.0	84.0	234.0	0.0	0.556291	0	.	.	none	.	LRP2	751	.	NM_004525	exon42	c.T7919C	p.I2640T	GTGTTGATTCCCC	.	PASS	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156900	26156900	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	104.0	41.0	117.0	0.0	0.394231	0	.	.	none	HIST1H1E,NS,carcinoma,+2,1	HIST1H1E	69	1	NM_005321	exon1	c.G282A	p.V94V	CCTGGTGCAGACC	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130116569	130116569	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	94.0	42.0	110.0	0.0	0.446809	0	.	.	none	.	COL6A5	205	.	NM_153264	exon9	c.G3711A	p.G1237G	CTGTGGGGCTGGC	.	PASS	Atlas-SNP
CHMP2B	25978	hgsc.bcm.edu	37	3	87295015	87295015	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	159.0	27.0	187.0	0.0	0.169811	0	.	.	none	.	CHMP2B	28	.	NM_014043	exon3	c.A278G	p.N93S	TGATGAATTCCCA	.	PASS	Atlas-SNP
ATP1A3	478	hgsc.bcm.edu	37	19	42485704	42485704	+	Missense_Mutation	SNP	G	G	A	rs150785666	bycluster;byfrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	78.0	34.0	112.0	0.0	0.435897	0	G|0.999;A|0.001	0.001	strong	.	ATP1A3	117	.	NM_001256214	exon11	c.C1426T	p.R476C	TGTTGCGTTCACG	.	PASS	Atlas-SNP
OR6N1	128372	hgsc.bcm.edu	37	1	158735736	158735736	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	94.0	35.0	99.0	0.0	0.37234	0	.	.	none	.	OR6N1	96	.	NM_001005185	exon1	c.C737T	p.T246I	ACCACAGTGAAGT	.	PASS	Atlas-SNP
GML	2765	hgsc.bcm.edu	37	8	143927837	143927837	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	162.0	67.0	184.0	0.0	0.41358	0	.	.	none	.	GML	34	.	NM_002066	exon4	c.T208C	p.Y70H	CTTGTTTATAAGA	.	PASS	Atlas-SNP
POLN	353497	hgsc.bcm.edu	37	4	2097647	2097647	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	108.0	17.0	108.0	0.0	0.157407	0	.	.	none	.	POLN	82	.	NM_181808	exon18	c.G1996A	p.V666M	GTTCCACGGGCAC	.	PASS	Atlas-SNP
IGSF11	152404	hgsc.bcm.edu	37	3	118649074	118649074	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	66.0	14.0	87.0	0.0	0.212121	0	.	.	none	.	IGSF11	122	.	NM_001015887	exon2	c.T101C	p.V34A	CGGGCCACCTGGA	.	PASS	Atlas-SNP
RPTN	126638	hgsc.bcm.edu	37	1	152128973	152128973	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	270.0	124.0	284.0	0.0	0.459259	0	.	.	none	.	RPTN	123	.	NM_001122965	exon3	c.G602T	p.S201I	TCTTGACTTTGTC	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101730422	101730422	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	107.0	38.0	109.0	1.0	0.35514	0.00917431	.	.	none	PABPC1,NS,carcinoma,+2,2	PABPC1	76	2	NM_002568	exon2	c.C280G	p.R94G	TTTTGCGAAGTGA	.	scavenged	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274867	203274867	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	53.0	14.0	69.0	0.0	0.264151	0	.	.	none	BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	NM_006763	exon1	c.G133C	p.A45P	CAGGAGGCACTCA	.	PASS	Atlas-SNP
NFATC1	4772	hgsc.bcm.edu	37	18	77156301	77156301	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	96.0	23.0	121.0	0.0	0.239583	0	.	.	none	.	NFATC1	105	.	NM_172390	exon1	c.C77G	p.T26S	GAGAAACTTTGGG	.	PASS	Atlas-SNP
IPO7	10527	hgsc.bcm.edu	37	11	9459505	9459505	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	218.0	23.0	227.0	0.0	0.105505	0	.	.	none	IPO7,NS,carcinoma,-1,1	IPO7	72	1	NM_006391	exon21	c.G2473A	p.V825I	AATGATGTTGACT	.	PASS	Atlas-SNP
DNASE1L2	1775	hgsc.bcm.edu	37	16	2287821	2287821	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	50.0	20.0	71.0	0.0	0.4	0	.	.	none	.	DNASE1L2	14	.	NM_001374	exon6	c.G645A	p.Q215Q	GGCGCAGGACTGG	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891202	44891202	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	66.0	3.0	77.0	0.0	0.0454545	0	.	.	none	ZNF285,NS,carcinoma,0,2	ZNF285	86	2	NM_152354	exon4	c.G1205C	p.C402S	TCACTGCATTTGT	.	scavenged	Atlas-SNP
LCA5	167691	hgsc.bcm.edu	37	6	80223259	80223259	+	Silent	SNP	T	T	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	165.0	113.0	282.0	0.0	0.684848	0	.	.	none	.	LCA5	71	.	NM_001122769	exon3	c.A390C	p.L130L	TTCTTTTAGCAGC	.	PASS	Atlas-SNP
FGG	2266	hgsc.bcm.edu	37	4	155526109	155526109	+	Silent	SNP	G	G	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	164.0	34.0	213.0	0.0	0.207317	0	.	.	none	.	FGG	71	.	NM_000509	exon9	c.C1239A	p.I413I	GAATGGGATTATC	.	PASS	Atlas-SNP
ST6GAL1	6480	hgsc.bcm.edu	37	3	186760492	186760492	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	105.0	58.0	159.0	1.0	0.552381	0.00628931	.	.	none	ST6GAL1,NS,carcinoma,-2,1	ST6GAL1	36	1	NM_003032	exon3	c.A1G	p.M1V	TTCATTATGATTC	.	scavenged	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	37	16	1255246	1255246	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	35.0	16.0	47.0	0.0	0.457143	0	.	.	none	.	CACNA1H	317	.	NM_021098	exon11	c.G2584A	p.G862S	TTCGACGGCATCA	.	PASS	Atlas-SNP
ALDH8A1	64577	hgsc.bcm.edu	37	6	135239666	135239666	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	51.0	39.0	115.0	0.0	0.764706	0	.	.	none	.	ALDH8A1	68	.	NM_022568	exon7	c.A1351T	p.R451W	GCTCCCTGATGAG	.	PASS	Atlas-SNP
CD97	976	hgsc.bcm.edu	37	19	14512523	14512523	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	57.0	22.0	65.0	0.0	0.385965	0	.	.	none	.	CD97	86	.	NM_078481	exon11	c.C1134T	p.S378S	GAGCAGCGCACGC	.	PASS	Atlas-SNP
HIST1H2BD	3017	hgsc.bcm.edu	37	6	26158526	26158526	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	121.0	20.0	112.0	0.0	0.165289	0	.	.	none	.	HIST1H2BD	45	.	NM_021063	exon1	c.C129T	p.Y43Y	TGTGTACAAGGTG	.	PASS	Atlas-SNP
EIF3B	8662	hgsc.bcm.edu	37	7	2409105	2409105	+	Splice_Site	SNP	A	A	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	366.0	128.0	484.0	0.0	0.349727	0	.	.	none	.	EIF3B	54	.	NM_003751	exon10	c.1404-2A>C	.	TTCTGCAGAGACT	.	PASS	Atlas-SNP
FAM105B	90268	hgsc.bcm.edu	37	5	14681631	14681631	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	116.0	36.0	194.0	0.0	0.310345	0	.	.	none	.	FAM105B	36	.	NM_138348	exon4	c.A383T	p.Y128F	ATAATTACTGTGC	.	PASS	Atlas-SNP
DLGAP2	9228	hgsc.bcm.edu	37	8	1497114	1497114	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	21.0	7.0	33.0	0.0	0.333333	0	.	.	none	.	DLGAP2	292	.	NM_004745	exon2	c.C255A	p.H85Q	GATGCACTACAGC	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138423	37138423	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	59.0	15.0	79.0	0.0	0.254237	0	.	.	none	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	NM_001243186	exon1	c.G345C	p.K115N	CACCAAGCTGGCG	.	PASS	Atlas-SNP
DKK2	27123	hgsc.bcm.edu	37	4	107845787	107845787	+	Silent	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	224.0	152.0	294.0	0.0	0.678571	0	.	.	none	.	DKK2	96	.	NM_014421	exon3	c.A444G	p.R148R	TCGATCTCTGTGC	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33041314	33041314	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	47.0	17.0	74.0	0.0	0.361702	0	.	.	none	.	HLA-DPA1	20	.	NM_033554	exon1	c.G34A	p.A12T	TCACAGCTCTGAT	.	PASS	Atlas-SNP
PIGF	5281	hgsc.bcm.edu	37	2	46839367	46839367	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	206.0	81.0	309.0	1.0	0.393204	0.00323625	.	.	none	.	PIGF	9	.	NM_002643	exon4	c.G437A	p.G146E	ACTTACCCATTTC	.	PASS	Atlas-SNP
POU3F3	5455	hgsc.bcm.edu	37	2	105473228	105473228	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	87.0	33.0	74.0	0.0	0.37931	0	.	.	none	.	POU3F3	43	.	NM_006236	exon1	c.G1260A	p.A420A	GGGCGCGCTGGAG	.	PASS	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	37	17	48631644	48631644	+	Missense_Mutation	SNP	G	G	A	rs200274697	by1000genomes	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	75.0	38.0	99.0	0.0	0.506667	0	G|1.000;A|0.000	0.000	strong	.	SPATA20	59	.	NM_022827	exon15	c.G1990A	p.V664M	AATTCCGTGTCAG	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140186856	140186856	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	92.0	30.0	110.0	1.0	0.326087	0.00909091	.	.	none	PCDHA4_ENST00000530339,colon,carcinoma,+1,5	PCDHA4	419	5	NM_031500	exon1	c.C84T	p.N28N	AGGGAACGGTCAG	.	scavenged	Atlas-SNP
SCNN1A	6337	hgsc.bcm.edu	37	12	6457289	6457289	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	107.0	49.0	71.0	0.0	0.457944	0	.	.	none	.	SCNN1A	54	.	NM_001159576	exon12	c.G1937A	p.R646K	CGGAACCTTCGGA	.	PASS	Atlas-SNP
RPUSD4	84881	hgsc.bcm.edu	37	11	126081386	126081386	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	74.0	36.0	80.0	0.0	0.486486	0	.	.	none	.	RPUSD4	36	.	NM_001144827	exon1	c.C148T	p.L50F	CTCGGAGCTTCTC	.	PASS	Atlas-SNP
FZD1	8321	hgsc.bcm.edu	37	7	90894950	90894950	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	60.0	13.0	37.0	0.0	0.216667	0	.	.	none	.	FZD1	64	.	NM_003505	exon1	c.A755G	p.Q252R	ACCCTCAGCACGG	.	PASS	Atlas-SNP
PLCH2	9651	hgsc.bcm.edu	37	1	2422698	2422698	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	39.0	7.0	50.0	0.0	0.179487	0	.	.	none	.	PLCH2	131	.	NM_014638	exon11	c.C1583T	p.S528L	AAGAGTCGAAGAT	.	PASS	Atlas-SNP
PDLIM5	10611	hgsc.bcm.edu	37	4	95575792	95575792	+	Splice_Site	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	200.0	45.0	172.0	0.0	0.225	0	.	.	none	.	PDLIM5	76	.	NM_006457	exon10	c.1464+1G>A	.	CTTGGAGTAAGTA	.	PASS	Atlas-SNP
DEPDC5	9681	hgsc.bcm.edu	37	22	32257381	32257381	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	115.0	38.0	109.0	0.0	0.330435	0	.	.	none	.	DEPDC5	266	.	NM_001242896	exon33	c.C3292T	p.R1098C	TTTGTCCGCAGCC	.	PASS	Atlas-SNP
TGFBR3	7049	hgsc.bcm.edu	37	1	92262875	92262875	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	147.0	63.0	143.0	0.0	0.428571	0	.	.	none	.	TGFBR3	103	.	NM_001195684	exon4	c.C215T	p.A72V	TGGCCTGCAGTGC	.	PASS	Atlas-SNP
MFSD6	54842	hgsc.bcm.edu	37	2	191301341	191301341	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	99.0	63.0	140.0	0.0	0.636364	0	.	.	none	MFSD6,caecum,carcinoma,0,1	MFSD6	58	1	NM_017694	exon3	c.C586T	p.R196C	AAAATGCGTGAGA	.	PASS	Atlas-SNP
PMF1-BGLAP	100527963	hgsc.bcm.edu	37	1	156182902	156182902	+	Silent	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	97.0	44.0	127.0	0.0	0.453608	0	.	.	none	.	.	.	.	NM_001199664	exon1	c.T96C	p.I32I	TACCATTTCGAGG	.	PASS	Atlas-SNP
VANGL1	81839	hgsc.bcm.edu	37	1	116206843	116206843	+	Missense_Mutation	SNP	C	C	T	rs199932833		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	96.0	34.0	115.0	0.0	0.354167	0	.	.	weak	.	VANGL1	65	.	NM_138959	exon4	c.C766T	p.R256C	GTGGTCCGCTCCA	.	PASS	Atlas-SNP
TAPT1	202018	hgsc.bcm.edu	37	4	16165117	16165117	+	Silent	SNP	T	T	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	209.0	45.0	234.0	0.0	0.215311	0	.	.	none	.	TAPT1	31	.	NM_153365	exon14	c.A1518G	p.Q506Q	AATAGGTTGTTTG	.	PASS	Atlas-SNP
RAB22A	57403	hgsc.bcm.edu	37	20	56928537	56928537	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	207.0	84.0	213.0	0.0	0.405797	0	.	.	none	.	RAB22A	15	.	NM_020673	exon5	c.G320A	p.G107D	AGCATGGCCCACC	.	PASS	Atlas-SNP
AIM1	202	hgsc.bcm.edu	37	6	106968969	106968969	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	65.0	56.0	130.0	0.0	0.861538	0	.	.	none	.	AIM1	161	.	NM_001624	exon2	c.T2662G	p.L888V	TGTGGTTTGAACA	.	PASS	Atlas-SNP
MAGI1	9223	hgsc.bcm.edu	37	3	65415776	65415776	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	49.0	30.0	70.0	0.0	0.612245	0	.	.	none	.	MAGI1	481	.	NM_001033057	exon12	c.G1586A	p.G529E	GTGTGTCCCAAAA	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138242	37138242	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	24.0	13.0	24.0	0.0	0.541667	0	.	.	none	.	PIM1	71	.	NM_001243186	exon1	c.G164C	p.S55T	CCCGCAGCCACAG	.	PASS	Atlas-SNP
CACNA2D3	55799	hgsc.bcm.edu	37	3	54798316	54798316	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	46.0	12.0	74.0	0.0	0.26087	0	.	.	none	CACNA2D3,caecum,carcinoma,-2,1	CACNA2D3	159	1	NM_018398	exon13	c.C1318T	p.R440W	CTTAGCCGGCCCA	.	PASS	Atlas-SNP
ETFDH	2110	hgsc.bcm.edu	37	4	159601621	159601621	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	339.0	209.0	374.0	0.0	0.616519	0	.	.	none	.	ETFDH	57	.	NM_004453	exon2	c.T37G	p.Y13D	GCAGCATATCAGT	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23913163	23913163	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	65.0	24.0	77.0	0.0	0.369231	0	.	.	none	.	SACS	871	.	NM_014363	exon10	c.T4852C	p.F1618L	GTTTGAACTGATT	.	PASS	Atlas-SNP
SLC1A6	6511	hgsc.bcm.edu	37	19	15073065	15073065	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	70.0	30.0	90.0	0.0	0.428571	0	.	.	none	.	SLC1A6	111	.	NM_001272087	exon8	c.C684A	p.F228L	CACTGAGAATGGA	.	PASS	Atlas-SNP
NGLY1	55768	hgsc.bcm.edu	37	3	25781094	25781094	+	Silent	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	155.0	14.0	107.0	0.0	0.0903226	0	.	.	none	.	NGLY1	57	.	NM_018297	exon5	c.C855T	p.A285A	CTGGCAGGCATCA	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296201	39296201	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	89.0	37.0	73.0	0.0	0.41573	0	.	.	none	.	KRTAP4-6	46	.	NM_030976	exon1	c.G539A	p.C180Y	GTGTGGCAGGAGA	.	PASS	Atlas-SNP
CEP112	201134	hgsc.bcm.edu	37	17	64125942	64125942	+	Splice_Site	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	290.0	141.0	349.0	0.0	0.486207	0	.	.	none	.	CEP112	192	.	NM_001199165	exon7	c.565-1G>T	.	AACTTCCTGAAAT	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549597	31549597	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	83.0	34.0	101.0	0.0	0.409639	0	.	.	none	LTB,NS,lymphoid_neoplasm,0,1	LTB	19	1	NM_002341	exon2	c.G202A	p.G68R	CCAGTCCTTGCTG	.	PASS	Atlas-SNP
APMAP	57136	hgsc.bcm.edu	37	20	24959519	24959519	+	Splice_Site	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	44.0	21.0	63.0	0.0	0.477273	0	.	.	none	.	APMAP	3	.	NM_020531	exon4	c.213-1G>A	.	TTGAAGCTGCAAA	.	PASS	Atlas-SNP
FOXD4	2298	hgsc.bcm.edu	37	9	117303	117303	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	16.0	5.0	20.0	0.0	0.3125	0	.	.	none	.	FOXD4	75	.	NM_207305	exon1	c.G817A	p.A273T	CATAGGCGGGGGC	.	PASS	Atlas-SNP
GRID1	2894	hgsc.bcm.edu	37	10	87614258	87614258	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	34.0	13.0	45.0	0.0	0.382353	0	.	.	none	GRID1,right_upper_lobe,carcinoma,0,2	GRID1	204	2	NM_017551	exon8	c.C1228T	p.R410C	CCTTGCGCATGTC	.	PASS	Atlas-SNP
KIF6	221458	hgsc.bcm.edu	37	6	39607449	39607449	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	126.0	48.0	151.0	0.0	0.380952	0	.	.	none	.	KIF6	233	.	NM_145027	exon4	c.G336A	p.E112E	GTAACGCTCTGCA	.	PASS	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	37	4	183650276	183650276	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	136.0	17.0	144.0	0.0	0.125	0	.	.	none	.	.	.	.	NM_001080477	exon13	c.T2527G	p.F843V	ATCAGTTTCCTTA	.	PASS	Atlas-SNP
SLITRK1	114798	hgsc.bcm.edu	37	13	84454425	84454425	+	Silent	SNP	C	C	A	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	106.0	33.0	111.0	0.0	0.311321	0	.	.	none	.	SLITRK1	196	.	NM_052910	exon1	c.G1218T	p.L406L	GTTGCCCAGATCC	.	PASS	Atlas-SNP
OR52R1	119695	hgsc.bcm.edu	37	11	4825232	4825232	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	36.0	12.0	31.0	0.0	0.333333	0	.	.	none	.	OR52R1	81	.	NM_001005177	exon1	c.G379A	p.V127M	TAGCCACGTAGCA	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	37	8	11990866	11990866	+	Missense_Mutation	SNP	T	T	A	rs183048633	by1000genomes	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	8.0	5.0	2.0	0.0	0.625	0	T|0.993;A|0.007	0.007	strong	.	.	.	.	NM_001256869	exon1	c.A653T	p.D218V	TAAGGGTCAAAGG	.	PASS	Atlas-SNP
DLG2	1740	hgsc.bcm.edu	37	11	83770527	83770527	+	Silent	SNP	C	C	T	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	84.0	20.0	81.0	0.0	0.238095	0	.	.	none	.	DLG2	448	.	NM_001142699	exon11	c.G750A	p.R250R	ATTGACCCTGCAA	.	PASS	Atlas-SNP
MAN2B2	23324	hgsc.bcm.edu	37	4	6612851	6612851	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	61.0	40.0	91.0	0.0	0.655738	0	.	.	none	.	MAN2B2	80	.	NM_015274	exon15	c.G2409C	p.W803C	CGACTGGGACCTG	.	PASS	Atlas-SNP