BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524484.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 = 889,545 number of mapped reads = 809,090 (90.96%) number of supplementary alignments = 1,905 (0.21%) number of secondary alignments = 0 number of mapped bases = 46,770,416 bp number of sequenced bases = 46,755,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,576 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2125 >>>>>>> ACTG content number of A's = 11,829,142 bp (25.3%) number of C's = 8,606,481 bp (18.41%) number of T's = 15,109,784 bp (32.32%) number of G's = 11,209,583 bp (23.97%) number of N's = 952 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 219,285 number of insertions = 3,066 mapped reads with insertion percentage = 0.38% number of deletions = 8,460 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.56% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1639X There is a 1.39% of reference with a coverageData >= 1X There is a 0.09% 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 4073300 0.01634218596390177 0.2524753011731312 chr2 243199373 3761429 0.015466442012578708 0.18797086042857902 chr3 198022430 2636214 0.013312704020448592 0.12308001106744042 chr4 191154276 2676613 0.014002370525051712 0.13482050151052102 chr5 180915260 2618837 0.014475489795609281 0.12829567900309147 chr6 171115067 2069253 0.012092757442569333 0.13392070801123018 chr7 159138663 2354402 0.014794657411442497 0.20264216335628496 chr8 146364022 4261689 0.02911705309655948 0.19784305005839686 chr9 141213431 2019792 0.014303115402670161 0.15076962341958164 chr10 135534747 2460855 0.01815663550838369 0.16559433658235365 chr11 135006516 1642808 0.012168360821932477 0.15589916038897692 chr12 133851895 2209713 0.016508641883628168 0.1377362132245795 chr13 115169878 1052471 0.00913842246147035 0.10286628857170195 chr14 107349540 1106552 0.010307934249182624 0.10966666673825881 chr15 102531392 1265912 0.01234657966996098 0.124047955826271 chr16 90354753 1472419 0.016295977257555008 0.13921609492830417 chr17 81195210 1651077 0.020334660135739535 0.15653660027740793 chr18 78077248 1136144 0.01455153747222238 0.23235311075266601 chr19 59128983 955160 0.01615383778882177 0.19950973315213144 chr20 63025520 1342753 0.021304909503325004 0.15622175227412022 chr21 48129895 650522 0.013515965492964403 0.1269557944202165 chr22 51304566 399394 0.00778476520004087 0.09390100060392376 chrMT 16571 4809 0.29020578118399615 0.6133214497056253 chrX 155270560 2796781 0.01801230703360637 0.15234056285840675 chrY 59373566 151517 0.002551926896221797 0.07558791012536382