/cemt/variants/A36005_3_lane_gembs

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SAMPLE A36005_3_lane_gembs




Variant counts

Type Total Pass %
SNPs 1163195268 774992169 66.63 %
Multiallelic 0 0 0.00 %



VCF Filtering Stats

Type #Sites % #Non-Variant Sites % #Variant Sites %
All 1163195268 100% 1141632800 98.15 % 21562468 1.85 %
Passed 777836012 66.87 % 772518980 67.67 % 5317032 0.68 %
Filtered 385359256 33.13 % 369113820 32.33 % 16245436 2.09 %
q20 338597314 87.87 % 334730404 90.68 % 3866910 23.80 %
q20,qd2 23018504 5.97 % 11570994 3.13 % 11447510 70.47 %
q20,mq40 12416539 3.22 % 12165342 3.30 % 251197 1.55 %
qd2 5739957 1.49 % 5537648 1.50 % 202309 1.25 %
q20,qd2,mq40 3368396 0.87 % 3107185 0.84 % 261211 1.61 %
mq40 2145891 0.56 % 1946321 0.53 % 199570 1.23 %
qd2,mq40 66634 0.02 % 55926 0.02 % 10708 0.07 %
fs60 1496 0.00 % 0 0.00 % 1496 0.01 %
q20,qd2,fs60 1481 0.00 % 0 0.00 % 1481 0.01 %
qd2,fs60,mq40 1303 0.00 % 0 0.00 % 1303 0.01 %
qd2,fs60 1236 0.00 % 0 0.00 % 1236 0.01 %
fs60,mq40 349 0.00 % 0 0.00 % 349 0.00 %
q20,qd2,fs60,mq40 146 0.00 % 0 0.00 % 146 0.00 %
q20,fs60 7 0.00 % 0 0.00 % 7 0.00 %
q20,fs60,mq40 3 0.00 % 0 0.00 % 3 0.00 %

Coverage and Quality




Coverage Variants Quality Variants
./IMG//A36005_3_lane_gembs_coverage_variants.png ./IMG//A36005_3_lane_gembs_quality_variant.png



Filtering Criteria Distribution




Phred scale strand bias estimated using Fisher's Exact Test.
./IMG//A36005_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//A36005_3_lane_gembs_qd_variant.png ./IMG//A36005_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//A36005_3_lane_gembs_rmsmq_variant.png ./IMG//A36005_3_lane_gembs_rmsmq_nonvariant.png



Mutations

Type Mutation Status # %
Transition A>G All 7288208 30.85 %
Transition G>A All 1827320 7.73 %
Transition T>C All 6503169 27.53 %
Transition C>T All 1855448 7.85 %
Transversion A>C All 455596 1.93 %
Transversion C>A All 1112485 4.71 %
Transversion T>G All 499484 2.11 %
Transversion G>T All 1079683 4.57 %
Transversion A>T All 1072691 4.54 %
Transversion T>A All 1121008 4.74 %
Transversion C>G All 422019 1.79 %
Transversion G>C All 388418 1.64 %
Transition A>G Passed 627165 18.52 %
Transition G>A Passed 512007 15.12 %
Transition T>C Passed 602779 17.80 %
Transition C>T Passed 515333 15.22 %
Transversion A>C Passed 139252 4.11 %
Transversion C>A Passed 153192 4.52 %
Transversion T>G Passed 141464 4.18 %
Transversion G>T Passed 152519 4.51 %
Transversion A>T Passed 139592 4.12 %
Transversion T>A Passed 140375 4.15 %
Transversion C>G Passed 131035 3.87 %
Transversion G>C Passed 130798 3.86 %
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 2.84 17474145 6151384
Passed 2.00 2257284 1128227
dbSNPAll 0 0 0
dbSNPPassed 0 0 0