BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173856.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,165,128 number of mapped reads = 3,076,978 (97.21%) number of supplementary alignments = 320,099 (10.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,543,174 number of mapped paired reads (second in pair) = 1,533,804 number of mapped paired reads (both in pair) = 3,019,630 number of mapped paired reads (singletons) = 57,348 number of mapped bases = 360,589,571 bp number of sequenced bases = 360,331,800 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,275,923 duplication rate = 62.51% >>>>>>> Insert size mean insert size = 945,651.5401 std insert size = 8,980,134.058 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 52.9522 >>>>>>> ACTG content number of A's = 108,598,067 bp (30.14%) number of C's = 70,308,054 bp (19.51%) number of T's = 108,491,075 bp (30.11%) number of G's = 72,930,441 bp (20.24%) number of N's = 4,163 bp (0%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 3,792,570 number of insertions = 42,309 mapped reads with insertion percentage = 1.32% number of deletions = 108,484 mapped reads with deletion percentage = 3.43% homopolymer indels = 41.48% >>>>>>> Coverage mean coverageData = 0.1165X std coverageData = 1.826X There is a 2.79% of reference with a coverageData >= 1X There is a 2.11% of reference with a coverageData >= 2X There is a 1.53% of reference with a coverageData >= 3X There is a 1.22% of reference with a coverageData >= 4X There is a 0.87% of reference with a coverageData >= 5X There is a 0.69% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 30248340 0.12135712993870534 1.2222598052678428 chr2 243199373 32858165 0.13510793467382828 5.256956498877662 chr3 198022430 24614933 0.12430376195262324 0.9678066352032547 chr4 191154276 24869449 0.13010145271351398 1.3015375275803869 chr5 180915260 23041231 0.12735924542794233 0.9730182709850267 chr6 171115067 21751004 0.12711331843150903 1.0377767279189114 chr7 159138663 19386495 0.12182140175451896 1.183759347220104 chr8 146364022 19519160 0.13336036912131316 1.6291324008833066 chr9 141213431 15751377 0.11154305145379549 1.144301145457028 chr10 135534747 18452495 0.13614586228577974 1.5415105972578125 chr11 135006516 16182186 0.1198622590927389 0.9591715234309798 chr12 133851895 15353126 0.11470234321299673 0.9236180826423563 chr13 115169878 11526429 0.10008197629592001 0.8730677077939951 chr14 107349540 10954024 0.10204071670917267 0.879007972188135 chr15 102531392 10724544 0.10459766312350466 0.8622011079731073 chr16 90354753 11380771 0.12595652826365428 1.1505792131714696 chr17 81195210 9368311 0.11538009446616371 0.9857502986361922 chr18 78077248 9791790 0.1254115667601399 1.5719818370330982 chr19 59128983 6631518 0.11215342567282106 1.0274036605838648 chr20 63025520 6937855 0.11008009136616406 0.9447435080732867 chr21 48129895 5267281 0.1094388633093839 1.0955642574421223 chr22 51304566 4414248 0.08604006122963792 0.8418871918505767 chrMT 16571 577958 34.87767787097942 31.598089084971164 chrX 155270560 7920546 0.05101125416176769 0.6143183647730164 chrY 59373566 3066335 0.051644784145186765 0.9963517870105333