BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524281.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 = 1,276,236 number of mapped reads = 1,186,993 (93.01%) number of supplementary alignments = 4,696 (0.37%) number of secondary alignments = 0 number of mapped bases = 70,199,796 bp number of sequenced bases = 70,178,828 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,219 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5125 >>>>>>> ACTG content number of A's = 18,513,150 bp (26.38%) number of C's = 13,600,430 bp (19.38%) number of T's = 22,024,764 bp (31.38%) number of G's = 16,030,764 bp (22.84%) number of N's = 9,720 bp (0.01%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 336,089 number of insertions = 5,318 mapped reads with insertion percentage = 0.45% number of deletions = 13,335 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.44% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 0.236X There is a 2.09% of reference with a coverageData >= 1X There is a 0.13% 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 5677179 0.022776990393135268 0.43942568593044 chr2 243199373 5924364 0.024360112145519388 0.2440227910285557 chr3 198022430 4675522 0.023611072745648057 0.16357271431796938 chr4 191154276 4618343 0.024160291344986706 0.1778330392707762 chr5 180915260 4296597 0.023749223807875575 0.16468309731350134 chr6 171115067 4084769 0.023871474742782294 0.17642880492908902 chr7 159138663 3879604 0.02437876457464017 0.3105223965569028 chr8 146364022 3633721 0.024826599804697907 0.24069634219550828 chr9 141213431 2939312 0.020814677323433915 0.21355253334634353 chr10 135534747 3353374 0.024741802926743207 0.23175630552278695 chr11 135006516 3190239 0.023630259446144067 0.2137448354168131 chr12 133851895 3140568 0.02346300737841627 0.16537611200290117 chr13 115169878 2228338 0.019348270908127557 0.1467038119079567 chr14 107349540 2140166 0.019936424506336963 0.15907835104368803 chr15 102531392 1963091 0.019146243523154353 0.14731683148643773 chr16 90354753 1977440 0.021885290306753426 0.16967749789730863 chr17 81195210 1838495 0.022642899747411207 0.16886364937939433 chr18 78077248 1886369 0.02416029058811089 0.40384416581623295 chr19 59128983 1327854 0.022456905778338858 0.31011518226891144 chr20 63025520 1426007 0.022625866474405922 0.16222769604319848 chr21 48129895 928803 0.01929783973141849 0.16106095377740198 chr22 51304566 816601 0.015916731465967376 0.13349761666790258 chrMT 16571 8868 0.5351517711664957 0.7657297492972011 chrX 155270560 4035672 0.025991224608193593 0.19134442148320882 chrY 59373566 208500 0.0035116637595929475 0.10178843832538483