BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524803.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 = 1,009,502 number of mapped reads = 922,971 (91.43%) number of supplementary alignments = 3,223 (0.32%) number of secondary alignments = 0 number of mapped bases = 52,811,286 bp number of sequenced bases = 52,794,553 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,455 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.597 >>>>>>> ACTG content number of A's = 12,236,227 bp (23.18%) number of C's = 9,287,018 bp (17.59%) number of T's = 17,610,075 bp (33.36%) number of G's = 13,654,671 bp (25.86%) number of N's = 6,562 bp (0.01%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 266,817 number of insertions = 3,657 mapped reads with insertion percentage = 0.39% number of deletions = 10,265 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.71% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.1725X There is a 1.56% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4271686 0.017138115776249158 0.21481736996426745 chr2 243199373 4473555 0.018394599232786673 0.2645288680196793 chr3 198022430 3440005 0.017371794700226637 0.14243840712329947 chr4 191154276 3315747 0.017345921155329007 0.15236663424906383 chr5 180915260 3147284 0.017396454008357282 0.14190511406952658 chr6 171115067 3005304 0.01756305889767147 0.1525530877635205 chr7 159138663 2908043 0.0182736422763587 0.19221843114106163 chr8 146364022 2598667 0.01775482092176997 0.1667120291426808 chr9 141213431 2219666 0.0157185190125435 0.1516120932531613 chr10 135534747 2556719 0.018863937525924624 0.1918134890553335 chr11 135006516 2384781 0.01766419185278435 0.16057633821114858 chr12 133851895 2384298 0.017812956626426544 0.14472187251743057 chr13 115169878 1623838 0.014099502649468814 0.12855319277827884 chr14 107349540 1568860 0.014614501375599746 0.13172564357818692 chr15 102531392 1544305 0.015061777372533867 0.13232409517192534 chr16 90354753 1600322 0.01771154197057016 0.15286105771576325 chr17 81195210 1530787 0.018853168801460086 0.15205691747421485 chr18 78077248 1384673 0.017734654274699845 0.22481149422335459 chr19 59128983 1165753 0.01971542449833781 0.18978491501057487 chr20 63025520 1162406 0.018443417840900003 0.1509778522853621 chr21 48129895 706612 0.014681353449867282 0.1374737755240456 chr22 51304566 691761 0.013483419779830122 0.12714197783172382 chrMT 16571 6952 0.4195280912437391 0.6790608482454416 chrX 155270560 2942261 0.018949252195651255 0.15489497897794924 chrY 59373566 177001 0.002981141472957848 0.09415783173164725