BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867835.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 = 22,222,151 number of mapped reads = 21,722,634 (97.75%) number of supplementary alignments = 55,334 (0.25%) number of secondary alignments = 0 number of mapped bases = 1,902,543,047 bp number of sequenced bases = 1,902,081,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,050,440 duplication rate = 1.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.2202 >>>>>>> ACTG content number of A's = 533,076,909 bp (28.03%) number of C's = 413,648,443 bp (21.75%) number of T's = 534,188,598 bp (28.08%) number of G's = 420,752,364 bp (22.12%) number of N's = 415,038 bp (0.02%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 8,501,184 number of insertions = 178,847 mapped reads with insertion percentage = 0.81% number of deletions = 185,214 mapped reads with deletion percentage = 0.83% homopolymer indels = 34.88% >>>>>>> Coverage mean coverageData = 0.6146X std coverageData = 7.0939X There is a 41.1% of reference with a coverageData >= 1X There is a 12.78% of reference with a coverageData >= 2X There is a 3.35% of reference with a coverageData >= 3X There is a 0.88% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 178801489 0.7173562428155394 19.252361406048376 chr2 243199373 156704973 0.6443477672946138 4.294955227570421 chr3 198022430 118654861 0.5991990957792004 2.600759978243842 chr4 191154276 118674791 0.6208325206389838 4.291830864594705 chr5 180915260 108536156 0.5999281431538721 1.0004396690292683 chr6 171115067 102720609 0.6003013691365939 2.0968339786154226 chr7 159138663 100231975 0.6298404995397001 4.716316767214656 chr8 146364022 92311199 0.6306959711724784 3.2882934593035382 chr9 141213431 69973657 0.49551700928504455 3.0149583090512873 chr10 135534747 100987785 0.7451062346395939 14.279572841852454 chr11 135006516 97064211 0.7189594537792532 3.4038097036989297 chr12 133851895 86607347 0.6470386317653553 1.0170314209764224 chr13 115169878 61073441 0.5302900555299711 0.8542884482554888 chr14 107349540 49373675 0.459933736092395 0.9838117719649224 chr15 102531392 54082821 0.5274757315301054 0.8301988685118146 chr16 90354753 54979669 0.6084867389322618 4.215721944861793 chr17 81195210 62548692 0.7703495317026706 2.224014190718997 chr18 78077248 49497403 0.6339542474652795 6.93736967787107 chr19 59128983 42776074 0.7234366604952431 10.946350060924004 chr20 63025520 41642916 0.66073101816534 1.5210206531842185 chr21 48129895 26218118 0.5447366548379131 3.1846664349883183 chr22 51304566 26047558 0.507704479948237 0.8775114087438035 chrMT 16571 1324756 79.94423993723976 27.26868871004834 chrX 155270560 92752893 0.5973630352077045 1.9611317599230655 chrY 59373566 8955978 0.150841167262886 6.925285651196906