BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716525.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 = 459,009 number of mapped reads = 411,153 (89.57%) number of supplementary alignments = 1,103 (0.24%) number of secondary alignments = 0 number of mapped bases = 23,592,842 bp number of sequenced bases = 23,585,514 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,559 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1326 >>>>>>> ACTG content number of A's = 5,925,612 bp (25.12%) number of C's = 4,342,633 bp (18.41%) number of T's = 7,683,641 bp (32.58%) number of G's = 5,633,419 bp (23.89%) number of N's = 209 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 116,225 number of insertions = 1,740 mapped reads with insertion percentage = 0.42% number of deletions = 4,607 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.49% >>>>>>> Coverage mean coverageData = 0.0076X std coverageData = 0.1X There is a 0.73% 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 1941315 0.007788606472519079 0.11800973107973413 chr2 243199373 1939193 0.007973675984764977 0.12074230889736058 chr3 198022430 1590225 0.008030529672825448 0.09280859867738903 chr4 191154276 1461186 0.007644014199295233 0.09334383139335407 chr5 180915260 1401949 0.00774920258246872 0.09089965266669568 chr6 171115067 1344431 0.007856882643770931 0.0966884172853891 chr7 159138663 1246188 0.007830831153834691 0.11434812129498481 chr8 146364022 1191642 0.008141631964718761 0.10101133319489874 chr9 141213431 976014 0.006911623016935266 0.0906504950224249 chr10 135534747 1129876 0.008336430509587331 0.1081604938942164 chr11 135006516 1084679 0.008034271471756222 0.09976630710527375 chr12 133851895 1080095 0.00806932916414818 0.09279057123409812 chr13 115169878 773105 0.006712736120116408 0.08438625389364358 chr14 107349540 707410 0.006589781381457247 0.0847885359384447 chr15 102531392 686978 0.006700172372574441 0.08449731368146386 chr16 90354753 739039 0.008179304081546214 0.09628020223447395 chr17 81195210 664861 0.008188426386236331 0.09539675159003132 chr18 78077248 627746 0.008040063092387683 0.12249214276388239 chr19 59128983 505037 0.008541276618946752 0.11210961792123765 chr20 63025520 497341 0.007891105063472702 0.09212012560667912 chr21 48129895 310202 0.006445100285383959 0.08457479865039078 chr22 51304566 287972 0.005612989689845539 0.07725621495500158 chrMT 16571 3443 0.2077726148090037 0.4875889436052171 chrX 155270560 1325622 0.008537497385209404 0.09881673339980201 chrY 59373566 77293 0.0013018082828307803 0.0481684504390996