BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716816.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 = 545,141 number of mapped reads = 483,624 (88.72%) number of supplementary alignments = 2,176 (0.4%) number of secondary alignments = 0 number of mapped bases = 27,898,942 bp number of sequenced bases = 27,891,137 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,417 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4795 >>>>>>> ACTG content number of A's = 6,977,338 bp (25.02%) number of C's = 5,026,542 bp (18.02%) number of T's = 9,111,797 bp (32.67%) number of G's = 6,775,263 bp (24.29%) number of N's = 197 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 139,438 number of insertions = 2,162 mapped reads with insertion percentage = 0.44% number of deletions = 4,993 mapped reads with deletion percentage = 1.02% homopolymer indels = 41.82% >>>>>>> Coverage mean coverageData = 0.009X std coverageData = 0.1167X There is a 0.86% 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 3311290 0.013284981945942674 0.17437589318988345 chr2 243199373 2742148 0.011275308674418335 0.1512067463099043 chr3 198022430 1760973 0.008892795629262807 0.09738137148172833 chr4 191154276 1146075 0.0059955498981356815 0.08163281988554785 chr5 180915260 2005987 0.011087992245651362 0.10822173789132263 chr6 171115067 1049597 0.006133866633731324 0.08501020249297188 chr7 159138663 1904213 0.01196574712959603 0.17280850996207292 chr8 146364022 1231236 0.008412149264386845 0.10496921943447968 chr9 141213431 1019041 0.007216317830277773 0.09652167194806693 chr10 135534747 1245376 0.009188610504433967 0.10928063355401836 chr11 135006516 1211782 0.008975729734407783 0.1131414129308204 chr12 133851895 1112955 0.008314824381081791 0.09393609322107806 chr13 115169878 811187 0.007043395496173053 0.0864883499421111 chr14 107349540 595536 0.005547634391353703 0.07758628079218484 chr15 102531392 1038697 0.010130526658606176 0.10413060988345363 chr16 90354753 799751 0.008851233315861093 0.09927685855267228 chr17 81195210 1046754 0.012891819603644106 0.12007857041869151 chr18 78077248 915712 0.011728282226340765 0.15897307538580618 chr19 59128983 434859 0.007354413655313504 0.11736294466559165 chr20 63025520 712405 0.011303437083898712 0.10985853032112174 chr21 48129895 354471 0.007364882055113563 0.08976635426972865 chr22 51304566 310867 0.006059246266696809 0.08009686992978308 chrMT 16571 14561 0.8787037595799891 1.0162064576152918 chrX 155270560 1060859 0.00683232545821951 0.08973385271208599 chrY 59373566 62610 0.0010545096786000693 0.037346531658357995