BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173994.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,621,850 number of mapped reads = 3,547,171 (97.94%) number of supplementary alignments = 455,719 (12.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,774,555 number of mapped paired reads (second in pair) = 1,772,616 number of mapped paired reads (both in pair) = 3,502,322 number of mapped paired reads (singletons) = 44,849 number of mapped bases = 397,780,700 bp number of sequenced bases = 397,509,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,780,311 duplication rate = 62.58% >>>>>>> Insert size mean insert size = 931,558.5651 std insert size = 8,588,174.1619 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 52.6512 >>>>>>> ACTG content number of A's = 119,779,965 bp (30.13%) number of C's = 78,238,239 bp (19.68%) number of T's = 118,591,122 bp (29.83%) number of G's = 80,897,276 bp (20.35%) number of N's = 2,847 bp (0%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 3,287,630 number of insertions = 42,062 mapped reads with insertion percentage = 1.14% number of deletions = 114,352 mapped reads with deletion percentage = 3.15% homopolymer indels = 40.57% >>>>>>> Coverage mean coverageData = 0.1285X std coverageData = 2.3235X There is a 2.88% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 1.5% of reference with a coverageData >= 3X There is a 1.21% of reference with a coverageData >= 4X There is a 0.89% of reference with a coverageData >= 5X There is a 0.76% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 31938510 0.1281381361132095 1.2625362685748651 chr2 243199373 36394556 0.14964905357712416 7.18571292662916 chr3 198022430 27454441 0.13864308704827025 1.1297731727146785 chr4 191154276 28048774 0.14673369901492553 1.3649983548808087 chr5 180915260 25863948 0.1429616716688244 1.1531809086038984 chr6 171115067 23335432 0.13637274852015224 1.201663575687041 chr7 159138663 21529332 0.1352866210771169 1.2682375153711463 chr8 146364022 20531745 0.14027863350188613 1.4619976000622974 chr9 141213431 17165812 0.12155934374259343 1.2071011328313228 chr10 135534747 19474283 0.1436847998838261 1.562276313415207 chr11 135006516 17781755 0.1317103464843134 1.1117764720286556 chr12 133851895 18285530 0.1366101690230086 1.1493776693624043 chr13 115169878 13400129 0.11635098719128625 1.0366190734266525 chr14 107349540 12525396 0.11667861827819663 1.0317629877442187 chr15 102531392 11150313 0.10875023524502622 0.9921842316330454 chr16 90354753 12110856 0.13403673407197517 1.25454102442225 chr17 81195210 10254444 0.1262937062420308 1.0933834584326492 chr18 78077248 11097779 0.14213844985929833 1.5771520216915578 chr19 59128983 7057346 0.11935510543112166 1.0867503266278047 chr20 63025520 8350582 0.1324952495433596 1.1112697388644155 chr21 48129895 5518826 0.11466524080303936 1.2030625969809956 chr22 51304566 4753773 0.09265789325651834 0.9940821441752942 chrMT 16571 571374 34.48035725061855 32.38746002902057 chrX 155270560 10279598 0.06620442407111818 0.7644534846885601 chrY 59373566 2906166 0.04894713583482589 0.8470788971403048