BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238658.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,121,660 number of mapped reads = 2,887,254 (92.49%) number of supplementary alignments = 21,239 (0.68%) number of secondary alignments = 0 number of mapped bases = 181,470,671 bp number of sequenced bases = 181,400,297 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,137,043 duplication rate = 21.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3069 >>>>>>> ACTG content number of A's = 45,374,282 bp (25.01%) number of C's = 32,056,794 bp (17.67%) number of T's = 61,047,612 bp (33.65%) number of G's = 42,917,193 bp (23.66%) number of N's = 4,416 bp (0%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 900,471 number of insertions = 12,496 mapped reads with insertion percentage = 0.43% number of deletions = 41,758 mapped reads with deletion percentage = 1.44% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.0586X std coverageData = 0.9447X There is a 1.54% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 7637316 0.030641111221143155 0.7046270717657951 chr2 243199373 27630101 0.1136109055675896 1.9966617107555575 chr3 198022430 20221442 0.10211692685520524 0.9266785261682157 chr4 191154276 10646242 0.05569450091715448 0.670426951804844 chr5 180915260 15873050 0.08773748549459012 0.8557742196773661 chr6 171115067 4357852 0.025467377457766473 0.7417491285620785 chr7 159138663 7879207 0.04951158223567582 0.7032207880143396 chr8 146364022 6553007 0.044771979551094875 0.6899050432920913 chr9 141213431 10168493 0.0720079735191761 0.8141280130329334 chr10 135534747 6824840 0.050354910095490125 0.687503205401993 chr11 135006516 8359789 0.06192137422463372 0.7296495424217097 chr12 133851895 7584815 0.056665727444501254 0.6932380454859224 chr13 115169878 3197992 0.02776760777674871 0.628809891363146 chr14 107349540 3876517 0.03611116545073225 0.5857230033708906 chr15 102531392 4282577 0.04176844687722566 0.690858811966158 chr16 90354753 8504882 0.09412766586833567 0.8906722458937842 chr17 81195210 8602613 0.10594975984420756 1.0047342237007706 chr18 78077248 3567813 0.04569593692646544 2.0181351461090866 chr19 59128983 1415670 0.023942065771704546 0.5795748491711806 chr20 63025520 1547675 0.02455632258170976 0.43296119416195317 chr21 48129895 2940635 0.06109788936792818 0.6998225487736964 chr22 51304566 2413175 0.04703626184071024 0.6177351260813382 chrMT 16571 43268 2.6110675276084727 4.60854384223883 chrX 155270560 6875376 0.04427997168297712 0.6047528744239586 chrY 59373566 466324 0.007854067582870128 0.3477558426848175