/EXTERNAL ENCODE/variants/K005731_K005712_2_lane_gembs

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SAMPLE K005731_K005712_2_lane_gembs




Variant counts

Type Total Pass %
SNPs 1170386671 1097498714 93.77 %
Multiallelic 0 0 0.00 %



VCF Filtering Stats

Type #Sites % #Non-Variant Sites % #Variant Sites %
All 1170386671 100% 1161239735 99.22 % 9146936 0.78 %
Passed 1098171894 93.83 % 1094652944 94.27 % 3518950 0.32 %
Filtered 72214777 6.17 % 66586791 5.73 % 5627986 0.51 %
q20 45184607 62.57 % 44734419 67.18 % 450188 8.00 %
q20,mq40 9427741 13.06 % 9282146 13.94 % 145595 2.59 %
q20,qd2 5609607 7.77 % 1596888 2.40 % 4012719 71.30 %
mq40 5032002 6.97 % 4696518 7.05 % 335484 5.96 %
qd2 4341277 6.01 % 3920576 5.89 % 420701 7.48 %
q20,qd2,mq40 2476512 3.43 % 2247166 3.37 % 229346 4.08 %
qd2,mq40 132530 0.18 % 109078 0.16 % 23452 0.42 %
fs60 3550 0.00 % 0 0.00 % 3550 0.06 %
qd2,fs60 2691 0.00 % 0 0.00 % 2691 0.05 %
qd2,fs60,mq40 1999 0.00 % 0 0.00 % 1999 0.04 %
q20,qd2,fs60 1386 0.00 % 0 0.00 % 1386 0.02 %
fs60,mq40 656 0.00 % 0 0.00 % 656 0.01 %
q20,qd2,fs60,mq40 175 0.00 % 0 0.00 % 175 0.00 %
q20,fs60 37 0.00 % 0 0.00 % 37 0.00 %
q20,fs60,mq40 7 0.00 % 0 0.00 % 7 0.00 %

Coverage and Quality




Coverage Variants Quality Variants
./IMG//K005731_K005712_2_lane_gembs_coverage_variants.png ./IMG//K005731_K005712_2_lane_gembs_quality_variant.png



Filtering Criteria Distribution




Phred scale strand bias estimated using Fisher's Exact Test.
./IMG//K005731_K005712_2_lane_gembs_fs_variant.png



Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants.
./IMG//K005731_K005712_2_lane_gembs_qd_variant.png ./IMG//K005731_K005712_2_lane_gembs_qd_nonvariant.png



Root Mean Square of the mapping quality of reads. Variants. Root Mean Square of the mapping quality of reads. Non-Variants.
./IMG//K005731_K005712_2_lane_gembs_rmsmq_variant.png ./IMG//K005731_K005712_2_lane_gembs_rmsmq_nonvariant.png



Mutations

Type Mutation Status # %
Transition A>G All 3384881 30.71 %
Transition G>A All 955424 8.67 %
Transition T>C All 3184039 28.89 %
Transition C>T All 986108 8.95 %
Transversion A>C All 271280 2.46 %
Transversion C>A All 373314 3.39 %
Transversion T>G All 282920 2.57 %
Transversion G>T All 366212 3.32 %
Transversion A>T All 337623 3.06 %
Transversion T>A All 347496 3.15 %
Transversion C>G All 269925 2.45 %
Transversion G>C All 263603 2.39 %
Transition A>G Passed 761706 18.01 %
Transition G>A Passed 647060 15.30 %
Transition T>C Passed 782622 18.50 %
Transition C>T Passed 650951 15.39 %
Transversion A>C Passed 176964 4.18 %
Transversion C>A Passed 184939 4.37 %
Transversion T>G Passed 178316 4.22 %
Transversion G>T Passed 177303 4.19 %
Transversion A>T Passed 161545 3.82 %
Transversion T>A Passed 164369 3.89 %
Transversion C>G Passed 172056 4.07 %
Transversion G>C Passed 172443 4.08 %
Transition A>G dbSNPAll 0 0.00 %
Transition G>A dbSNPAll 0 0.00 %
Transition T>C dbSNPAll 0 0.00 %
Transition C>T dbSNPAll 0 0.00 %
Transversion A>C dbSNPAll 0 0.00 %
Transversion C>A dbSNPAll 0 0.00 %
Transversion T>G dbSNPAll 0 0.00 %
Transversion G>T dbSNPAll 0 0.00 %
Transversion A>T dbSNPAll 0 0.00 %
Transversion T>A dbSNPAll 0 0.00 %
Transversion C>G dbSNPAll 0 0.00 %
Transversion G>C dbSNPAll 0 0.00 %
Transition A>G dbSNPPassed 0 0.00 %
Transition G>A dbSNPPassed 0 0.00 %
Transition T>C dbSNPPassed 0 0.00 %
Transition C>T dbSNPPassed 0 0.00 %
Transversion A>C dbSNPPassed 0 0.00 %
Transversion C>A dbSNPPassed 0 0.00 %
Transversion T>G dbSNPPassed 0 0.00 %
Transversion G>T dbSNPPassed 0 0.00 %
Transversion A>T dbSNPPassed 0 0.00 %
Transversion T>A dbSNPPassed 0 0.00 %
Transversion C>G dbSNPPassed 0 0.00 %
Transversion G>C dbSNPPassed 0 0.00 %



Ti/Tv Ratio

Status Ratio Transitions Transversions
All 3.39 8510452 2512373
Passed 2.05 2842339 1387935
dbSNPAll 0 0 0
dbSNPPassed 0 0 0