/CEMT/variants/A36002_3_lane_gembs

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SAMPLE A36002_3_lane_gembs




Variant counts

Type Total Pass %
SNPs 1160217967 840233507 72.42 %
Multiallelic 0 0 0.00 %



VCF Filtering Stats

Type #Sites % #Non-Variant Sites % #Variant Sites %
All 1160217967 100% 1141655346 98.40 % 18562621 1.60 %
Passed 842428178 72.61 % 837512892 73.36 % 4915286 0.58 %
Filtered 317789789 27.39 % 304142454 26.64 % 13647335 1.62 %
q20 276929122 87.14 % 274074173 90.11 % 2854949 20.92 %
q20,qd2 19703627 6.20 % 9769126 3.21 % 9934501 72.79 %
q20,mq40 11023355 3.47 % 10820173 3.56 % 203182 1.49 %
qd2 4991001 1.57 % 4750249 1.56 % 240752 1.76 %
q20,qd2,mq40 3054816 0.96 % 2830825 0.93 % 223991 1.64 %
mq40 2021462 0.64 % 1849742 0.61 % 171720 1.26 %
qd2,mq40 57638 0.02 % 48166 0.02 % 9472 0.07 %
fs60 3403 0.00 % 0 0.00 % 3403 0.02 %
q20,qd2,fs60 2321 0.00 % 0 0.00 % 2321 0.02 %
qd2,fs60 1505 0.00 % 0 0.00 % 1505 0.01 %
qd2,fs60,mq40 1081 0.00 % 0 0.00 % 1081 0.01 %
fs60,mq40 328 0.00 % 0 0.00 % 328 0.00 %
q20,qd2,fs60,mq40 120 0.00 % 0 0.00 % 120 0.00 %
q20,fs60 8 0.00 % 0 0.00 % 8 0.00 %
q20,fs60,mq40 2 0.00 % 0 0.00 % 2 0.00 %

Coverage and Quality




Coverage Variants Quality Variants
./IMG//A36002_3_lane_gembs_coverage_variants.png ./IMG//A36002_3_lane_gembs_quality_variant.png



Filtering Criteria Distribution




Phred scale strand bias estimated using Fisher's Exact Test.
./IMG//A36002_3_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//A36002_3_lane_gembs_qd_variant.png ./IMG//A36002_3_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//A36002_3_lane_gembs_rmsmq_variant.png ./IMG//A36002_3_lane_gembs_rmsmq_nonvariant.png



Mutations

Type Mutation Status # %
Transition A>G All 5864955 28.67 %
Transition G>A All 1619408 7.92 %
Transition T>C All 5735413 28.04 %
Transition C>T All 1631332 7.97 %
Transversion A>C All 412312 2.02 %
Transversion C>A All 1002494 4.90 %
Transversion T>G All 418392 2.05 %
Transversion G>T All 1000828 4.89 %
Transversion A>T All 1048609 5.13 %
Transversion T>A All 1053273 5.15 %
Transversion C>G All 337011 1.65 %
Transversion G>C All 332015 1.62 %
Transition A>G Passed 633198 16.98 %
Transition G>A Passed 571129 15.31 %
Transition T>C Passed 633009 16.97 %
Transition C>T Passed 570707 15.30 %
Transversion A>C Passed 157736 4.23 %
Transversion C>A Passed 192475 5.16 %
Transversion T>G Passed 158872 4.26 %
Transversion G>T Passed 188802 5.06 %
Transversion A>T Passed 171568 4.60 %
Transversion T>A Passed 173991 4.66 %
Transversion C>G Passed 139224 3.73 %
Transversion G>C Passed 139361 3.74 %
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 2.65 14851108 5604934
Passed 1.82 2408043 1322029
dbSNPAll 0 0 0
dbSNPPassed 0 0 0