/cemt/variants/A54778_3_lane_gembs

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SAMPLE A54778_3_lane_gembs




Variant counts

Type Total Pass %
SNPs 1159210460 635941195 54.86 %
Multiallelic 0 0 0.00 %



VCF Filtering Stats

Type #Sites % #Non-Variant Sites % #Variant Sites %
All 1159210460 100% 1138002361 98.17 % 21208099 1.83 %
Passed 639337458 55.15 % 633893760 55.70 % 5443698 0.85 %
Filtered 519873002 44.85 % 504108601 44.30 % 15764401 2.47 %
q20 463500461 89.16 % 459087903 91.07 % 4412558 27.99 %
q20,qd2 25414110 4.89 % 14879689 2.95 % 10534421 66.82 %
qd2 14765391 2.84 % 14535956 2.88 % 229435 1.46 %
q20,mq40 10995388 2.12 % 10805763 2.14 % 189625 1.20 %
q20,qd2,mq40 3414301 0.66 % 3207791 0.64 % 206510 1.31 %
mq40 1696860 0.33 % 1535903 0.30 % 160957 1.02 %
qd2,mq40 66331 0.01 % 55596 0.01 % 10735 0.07 %
q20,qd2,fs60 6482 0.00 % 0 0.00 % 6482 0.04 %
fs60 6153 0.00 % 0 0.00 % 6153 0.04 %
qd2,fs60 5408 0.00 % 0 0.00 % 5408 0.03 %
qd2,fs60,mq40 1465 0.00 % 0 0.00 % 1465 0.01 %
fs60,mq40 390 0.00 % 0 0.00 % 390 0.00 %
q20,qd2,fs60,mq40 244 0.00 % 0 0.00 % 244 0.00 %
q20,fs60 14 0.00 % 0 0.00 % 14 0.00 %
q20,fs60,mq40 4 0.00 % 0 0.00 % 4 0.00 %

Coverage and Quality




Coverage Variants Quality Variants
./IMG//A54778_3_lane_gembs_coverage_variants.png ./IMG//A54778_3_lane_gembs_quality_variant.png



Filtering Criteria Distribution




Phred scale strand bias estimated using Fisher's Exact Test.
./IMG//A54778_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//A54778_3_lane_gembs_qd_variant.png ./IMG//A54778_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//A54778_3_lane_gembs_rmsmq_variant.png ./IMG//A54778_3_lane_gembs_rmsmq_nonvariant.png



Mutations

Type Mutation Status # %
Transition A>G All 7045065 29.18 %
Transition G>A All 2184515 9.05 %
Transition T>C All 5964987 24.70 %
Transition C>T All 2216641 9.18 %
Transversion A>C All 431734 1.79 %
Transversion C>A All 1301890 5.39 %
Transversion T>G All 488809 2.02 %
Transversion G>T All 1256130 5.20 %
Transversion A>T All 1215568 5.03 %
Transversion T>A All 1262255 5.23 %
Transversion C>G All 416833 1.73 %
Transversion G>C All 363020 1.50 %
Transition A>G Passed 535548 18.59 %
Transition G>A Passed 434237 15.07 %
Transition T>C Passed 506833 17.59 %
Transition C>T Passed 436462 15.15 %
Transversion A>C Passed 118783 4.12 %
Transversion C>A Passed 133448 4.63 %
Transversion T>G Passed 120423 4.18 %
Transversion G>T Passed 131169 4.55 %
Transversion A>T Passed 119846 4.16 %
Transversion T>A Passed 122420 4.25 %
Transversion C>G Passed 110974 3.85 %
Transversion G>C Passed 110435 3.83 %
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 2.58 17411208 6736239
Passed 1.98 1913080 967498
dbSNPAll 0 0 0
dbSNPPassed 0 0 0