BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716872.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 = 431,450 number of mapped reads = 337,483 (78.22%) number of supplementary alignments = 549 (0.13%) number of secondary alignments = 0 number of mapped bases = 18,027,680 bp number of sequenced bases = 18,023,011 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,088 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7587 >>>>>>> ACTG content number of A's = 3,819,526 bp (21.19%) number of C's = 3,243,007 bp (17.99%) number of T's = 5,896,638 bp (32.72%) number of G's = 5,063,517 bp (28.09%) number of N's = 323 bp (0%) GC percentage = 46.09% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 116,152 number of insertions = 1,125 mapped reads with insertion percentage = 0.33% number of deletions = 2,653 mapped reads with deletion percentage = 0.78% homopolymer indels = 39.97% >>>>>>> Coverage mean coverageData = 0.0058X std coverageData = 0.0849X There is a 0.54% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 1824095 0.007318316771615987 0.09628316194237896 chr2 243199373 1531602 0.006297721828419352 0.1017095240805317 chr3 198022430 1233864 0.0062309305062057865 0.0847179041614707 chr4 191154276 1102940 0.00576989446995159 0.08190849559073136 chr5 180915260 1168352 0.006458006914397381 0.08600939879986122 chr6 171115067 770286 0.004501567357595693 0.07534688580843829 chr7 159138663 920852 0.005786475659909245 0.082595426940549 chr8 146364022 1137584 0.007772292565176981 0.09567553211530716 chr9 141213431 768754 0.005443915600351074 0.07931978111700208 chr10 135534747 918882 0.006779678424455981 0.09287405700349008 chr11 135006516 776865 0.0057542778157463155 0.08444707130816016 chr12 133851895 872441 0.00651795777713868 0.08618821657714495 chr13 115169878 308019 0.002674475351966597 0.05526369540897542 chr14 107349540 572404 0.005332151399996684 0.07856622277670929 chr15 102531392 372952 0.003637442082128369 0.06436034619365687 chr16 90354753 537580 0.005949659338894989 0.08463315999393732 chr17 81195210 718223 0.008845632642615248 0.10166156086382815 chr18 78077248 515631 0.006604113403177325 0.09007285886797939 chr19 59128983 455783 0.007708284108319603 0.10654086165757325 chr20 63025520 525429 0.008336765805343612 0.09978314145191172 chr21 48129895 250146 0.005197310320332093 0.07820570255821525 chr22 51304566 180772 0.0035235070500352736 0.06444582768373748 chrMT 16571 2865 0.17289240238971698 0.46056280898193885 chrX 155270560 513170 0.0033050051471444426 0.061116287978405966 chrY 59373566 48189 8.116238125228995E-4 0.03480342115522476