BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173947.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 = 11,573,660 number of mapped reads = 11,287,444 (97.53%) number of supplementary alignments = 1,485,034 (12.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,656,056 number of mapped paired reads (second in pair) = 5,631,388 number of mapped paired reads (both in pair) = 11,102,776 number of mapped paired reads (singletons) = 184,668 number of mapped bases = 1,280,279,106 bp number of sequenced bases = 1,279,437,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,225,596 duplication rate = 66.71% >>>>>>> Insert size mean insert size = 1,185,632.9299 std insert size = 10,153,355.8007 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.651 >>>>>>> ACTG content number of A's = 380,746,696 bp (29.76%) number of C's = 255,119,398 bp (19.94%) number of T's = 377,507,535 bp (29.51%) number of G's = 266,054,760 bp (20.79%) number of N's = 9,488 bp (0%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 11,112,228 number of insertions = 137,788 mapped reads with insertion percentage = 1.17% number of deletions = 365,206 mapped reads with deletion percentage = 3.16% homopolymer indels = 40.68% >>>>>>> Coverage mean coverageData = 0.4136X std coverageData = 7.3302X There is a 8.26% of reference with a coverageData >= 1X There is a 6.42% of reference with a coverageData >= 2X There is a 4.94% of reference with a coverageData >= 3X There is a 4.01% of reference with a coverageData >= 4X There is a 3.07% of reference with a coverageData >= 5X There is a 2.53% of reference with a coverageData >= 6X There is a 1.92% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.26% of reference with a coverageData >= 9X There is a 1.11% of reference with a coverageData >= 10X There is a 0.85% of reference with a coverageData >= 11X There is a 0.77% of reference with a coverageData >= 12X There is a 0.58% of reference with a coverageData >= 13X There is a 0.53% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.37% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 107837600 0.43264726710550505 3.314760801918043 chr2 243199373 117531435 0.48327194906049364 24.45082087837889 chr3 198022430 81743930 0.4128013680066445 1.9720481983559361 chr4 191154276 85063250 0.4449978926968916 2.784941029663869 chr5 180915260 76785499 0.42442798357639927 2.0020868515720944 chr6 171115067 73856501 0.43161892342303204 2.624122989302012 chr7 159138663 72841338 0.4577224454876814 3.1620837518893827 chr8 146364022 64597830 0.4413504706778282 3.873864529395982 chr9 141213431 55454422 0.39269934599917766 3.197217826225701 chr10 135534747 63052394 0.4652120241903724 3.646583480286163 chr11 135006516 59079058 0.43760153028465676 2.2081327541487266 chr12 133851895 58511477 0.4371359628490878 2.234589843298009 chr13 115169878 41640238 0.3615549371338224 1.8443887324250405 chr14 107349540 40049217 0.37307301922299807 1.9468274402927814 chr15 102531392 38242400 0.3729823545163612 1.9839846997828556 chr16 90354753 40111670 0.4439353622050187 2.561798075616691 chr17 81195210 36696826 0.4519580157499439 2.389783273776128 chr18 78077248 34312377 0.43946703910465695 3.858432017614538 chr19 59128983 24548821 0.41517407799826356 2.5938644637193167 chr20 63025520 27905894 0.4427713408790598 2.1555351122513984 chr21 48129895 18337736 0.3810051112723184 2.5950947640797617 chr22 51304566 16613698 0.3238249398698744 2.0908155220238056 chrMT 16571 2003566 120.9079717578903 90.27409257350506 chrX 155270560 34430893 0.22174772216961156 1.4894540447136868 chrY 59373566 9031036 0.15210533253131536 2.223608240094022