/CEMT/variants/A95338_2_lane_gembs

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SAMPLE A95338_2_lane_gembs




Variant counts

Type Total Pass %
SNPs 1164224675 1104169714 94.84 %
Multiallelic 0 0 0.00 %



VCF Filtering Stats

Type #Sites % #Non-Variant Sites % #Variant Sites %
All 1164224675 100% 1155313210 99.23 % 8911465 0.77 %
Passed 1104751889 94.89 % 1101283293 95.32 % 3468596 0.31 %
Filtered 59472786 5.11 % 54029917 4.68 % 5442869 0.49 %
q20 34051993 57.26 % 33633797 62.25 % 418196 7.68 %
q20,mq40 10009259 16.83 % 9872389 18.27 % 136870 2.51 %
q20,qd2 5654841 9.51 % 1698333 3.14 % 3956508 72.69 %
mq40 4549316 7.65 % 4228730 7.83 % 320586 5.89 %
qd2 2664891 4.48 % 2300235 4.26 % 364656 6.70 %
q20,qd2,mq40 2426528 4.08 % 2207332 4.09 % 219196 4.03 %
qd2,mq40 108131 0.18 % 89101 0.16 % 19030 0.35 %
fs60 2300 0.00 % 0 0.00 % 2300 0.04 %
qd2,fs60,mq40 1937 0.00 % 0 0.00 % 1937 0.04 %
qd2,fs60 1661 0.00 % 0 0.00 % 1661 0.03 %
q20,qd2,fs60 1070 0.00 % 0 0.00 % 1070 0.02 %
fs60,mq40 646 0.00 % 0 0.00 % 646 0.01 %
q20,qd2,fs60,mq40 203 0.00 % 0 0.00 % 203 0.00 %
q20,fs60 5 0.00 % 0 0.00 % 5 0.00 %
q20,fs60,mq40 5 0.00 % 0 0.00 % 5 0.00 %

Coverage and Quality




Coverage Variants Quality Variants
./IMG//A95338_2_lane_gembs_coverage_variants.png ./IMG//A95338_2_lane_gembs_quality_variant.png



Filtering Criteria Distribution




Phred scale strand bias estimated using Fisher's Exact Test.
./IMG//A95338_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//A95338_2_lane_gembs_qd_variant.png ./IMG//A95338_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//A95338_2_lane_gembs_rmsmq_variant.png ./IMG//A95338_2_lane_gembs_rmsmq_nonvariant.png



Mutations

Type Mutation Status # %
Transition A>G All 3201943 30.05 %
Transition G>A All 899662 8.44 %
Transition T>C All 3186756 29.91 %
Transition C>T All 902223 8.47 %
Transversion A>C All 303485 2.85 %
Transversion C>A All 345075 3.24 %
Transversion T>G All 310086 2.91 %
Transversion G>T All 340653 3.20 %
Transversion A>T All 317004 2.98 %
Transversion T>A All 320407 3.01 %
Transversion C>G All 266115 2.50 %
Transversion G>C All 262159 2.46 %
Transition A>G Passed 748994 17.86 %
Transition G>A Passed 649526 15.49 %
Transition T>C Passed 752675 17.95 %
Transition C>T Passed 649765 15.50 %
Transversion A>C Passed 185768 4.43 %
Transversion C>A Passed 185578 4.43 %
Transversion T>G Passed 186177 4.44 %
Transversion G>T Passed 176989 4.22 %
Transversion A>T Passed 152792 3.64 %
Transversion T>A Passed 155004 3.70 %
Transversion C>G Passed 175140 4.18 %
Transversion G>C Passed 174846 4.17 %
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 3.32 8190584 2464984
Passed 2.01 2800960 1392294
dbSNPAll 0 0 0
dbSNPPassed 0 0 0