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date Wed, 16 Jul 2014 20:31:41 -0400
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#Variant Level Analysis Report
#2014-07-15 03:23:43.461879
#Analysis done at http://www.cravat.us.
#Input file: dataset_346.dat
#This report shows analysis results at variant level.
#Input coordinate was hg19 genomic.
#Tissue type for CHASM analysis: Other
#For more information on CRAVAT, visit http://www.cravat.us.
#
ID	Chromosome	Position	Strand	Reference base	Alternate base	Sample ID	HUGO symbol	Transcript	Transcript strand	Codon change	Amino acid position	Sequence Ontology	Reference amino acid(s)	Alternate amino acid(s)	Other transcripts	Mappability Warning	Driver score of representative transcript (driver mutations close to 0)	Empirical p-value	FDR (Benjamini-Hochberg) (not available with less than 10 unique mutations)	Best driver score and transcript	All transcripts and driver scores	dbSNP	1000 Genomes allele frequency	ESP6500 allele frequency (European American)	ESP6500 allele frequency (African American)	Occurrences in study [exact nucleotide change]	Transcript in COSMIC	Protein sequence change in COSMIC	Occurrences in COSMIC [exact nucleotide change]	Occurrences in COSMIC by primary sites [exact nucleotide change]	MuPIT Link
TR1	chr22	30421786	+	A	T	No_sample_ID	MTMR3	NM_021090.3	+	aAc>aTc	1198	MS	N	I	NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I		0.6(NM_021090.3:N1198I)	0.3364	0.60	0.572(ENST00000323630:N1062I)	ENST00000323630:N1062I(0.572),ENST00000406629:N1170I(0.602),ENST00000401950:N1198I(0.6),ENST00000351488:N1161I(0.572),NM_153050.2:N1170I(0.572),ENST00000333027:N1170I(0.572),NM_021090.3:N1198I(0.6),NM_153051.2:N1161I(0.572)	rs75623810	0.00778388278388	0	0.0226963	1					 
TR2	chr22	29446079	+	A	G	No_sample_ID	ZNRF3	NM_001206998.1	+	cAc>cGc	637	MS	H	R	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R		0.514(NM_001206998.1:H637R)	0.1710	0.60	0.442(ENST00000544604:H637R)	ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514)	rs62641746	0	0.00598145	0.00104004	2					 
TR3	chr22	29446079	+	A	G	No_sample_ID	ZNRF3	NM_001206998.1	+	cAc>cGc	637	MS	H	R	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R		0.514(NM_001206998.1:H637R)	0.1710	0.60	0.442(ENST00000544604:H637R)	ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514)	rs62641746	0	0.00598145	0.00104004	2					 
TR4	chr22	40814500	-	A	G	No_sample_ID	MKL1	NM_020831.3	-	Agc>Ggc	648	MS	S	G	ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G		0.728(NM_020831.3:S648G)	0.6890	0.80	0.708(ENST00000402042:S598G)	ENST00000407029:S648G(0.728),NM_020831.3:S648G(0.728),ENST00000396617:S648G(0.728),ENST00000355630:S648G(0.728),ENST00000402042:S598G(0.708)	rs878756	0.419871794872	0.396977	0.860645	1					 
TR5	chr22	40815256	+	C	T	No_sample_ID	MKL1	NM_020831.3	-	Gcc>Acc	396	MS	A	T	ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T		0.748(NM_020831.3:A396T)	0.7476	0.80	0.748(ENST00000407029:A396T)	ENST00000407029:A396T(0.748),NM_020831.3:A396T(0.748),ENST00000396617:A396T(0.748),ENST00000355630:A396T(0.748),ENST00000402042:A346T(0.754)	rs34736200	0.0201465201465	0.00127937	0.0834091	1