BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716680.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,109,069 number of mapped reads = 2,808,775 (90.34%) number of supplementary alignments = 16,694 (0.54%) number of secondary alignments = 0 number of mapped bases = 163,011,501 bp number of sequenced bases = 162,965,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,626 duplication rate = 5.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5634 >>>>>>> ACTG content number of A's = 41,540,180 bp (25.49%) number of C's = 32,682,387 bp (20.05%) number of T's = 49,999,998 bp (30.68%) number of G's = 38,741,324 bp (23.77%) number of N's = 1,139 bp (0%) GC percentage = 43.83% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 805,921 number of insertions = 10,493 mapped reads with insertion percentage = 0.37% number of deletions = 29,279 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.16% >>>>>>> Coverage mean coverageData = 0.0527X std coverageData = 0.4208X There is a 4.31% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% 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 21871078 0.08774733604374851 0.6897782331442474 chr2 243199373 16184211 0.0665470917969842 0.6360814982054105 chr3 198022430 9904861 0.050018884224378016 0.26586506370339014 chr4 191154276 6600233 0.03452830424782127 0.25993666423099326 chr5 180915260 11627467 0.06427023900581963 0.302597367392969 chr6 171115067 5904361 0.03450520812407478 0.26494796039172314 chr7 159138663 10661445 0.06699468751977639 0.68623427078655 chr8 146364022 7076372 0.0483477558439874 0.34781241807546526 chr9 141213431 4414669 0.0312623874991041 0.3060680647542111 chr10 135534747 7255173 0.053529985192653215 0.35306858998129936 chr11 135006516 6828375 0.050578114318571114 0.40201818604471373 chr12 133851895 6256083 0.04673884519901642 0.25898262998495203 chr13 115169878 4552100 0.03952509179526959 0.23567054224728468 chr14 107349540 3407443 0.0317415705740332 0.22377338231357263 chr15 102531392 7033525 0.06859874681112298 0.3148371457827921 chr16 90354753 4929601 0.05455829202477041 0.2948895628938743 chr17 81195210 6251067 0.07698812528473047 0.36750310958786914 chr18 78077248 5066229 0.06488739203512911 0.7207576232130352 chr19 59128983 2561755 0.04332486151503739 0.4947768112642543 chr20 63025520 4314828 0.0684616009514876 0.31700542386668107 chr21 48129895 2038991 0.04236433509775993 0.26679419394337434 chr22 51304566 1974681 0.03848938123752962 0.23154788826832048 chrMT 16571 3278 0.19781546074467443 0.45704780852179294 chrX 155270560 5906081 0.03803735234805619 0.26942510881276865 chrY 59373566 387594 0.006528056610243016 0.16142464596900372