BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524648.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 = 1,325,372 number of mapped reads = 1,222,668 (92.25%) number of supplementary alignments = 5,434 (0.41%) number of secondary alignments = 0 number of mapped bases = 71,146,389 bp number of sequenced bases = 71,122,932 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,828 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7483 >>>>>>> ACTG content number of A's = 17,974,527 bp (25.27%) number of C's = 13,945,343 bp (19.61%) number of T's = 22,298,681 bp (31.35%) number of G's = 16,903,776 bp (23.77%) number of N's = 605 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 364,787 number of insertions = 4,576 mapped reads with insertion percentage = 0.37% number of deletions = 14,061 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.85% >>>>>>> Coverage mean coverageData = 0.023X std coverageData = 0.2253X There is a 2.03% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7275240 0.029188452854446448 0.38553501136686863 chr2 243199373 6283506 0.025836851150105554 0.27010035153262824 chr3 198022430 4514885 0.0227998666615696 0.16719853299675125 chr4 191154276 3259653 0.017052472318223214 0.17539164953891345 chr5 180915260 4377993 0.02419913610383115 0.17147516721122405 chr6 171115067 4603937 0.026905503300887 0.18992996393872227 chr7 159138663 4317635 0.027131276074626818 0.26457024208867347 chr8 146364022 6247752 0.04268639187846314 0.2995185815630347 chr9 141213431 2582072 0.018284889629230805 0.18278482948073332 chr10 135534747 3061225 0.022586274499778274 0.25156831561402987 chr11 135006516 3627318 0.026867725406675928 0.2074959326181537 chr12 133851895 2134426 0.015946176929359124 0.14386750874823695 chr13 115169878 1729658 0.015018319286575956 0.1352408563800492 chr14 107349540 1312610 0.012227439446876065 0.1259431930918605 chr15 102531392 1846111 0.01800532465218067 0.14891364804928411 chr16 90354753 2131018 0.023585012733087767 0.17796270974537118 chr17 81195210 1650081 0.020322393402270898 0.16303531309773134 chr18 78077248 1874565 0.024009106980819817 0.293159838387639 chr19 59128983 1515074 0.02562320410618258 0.2843353485011255 chr20 63025520 1358597 0.021556299733822108 0.16550519096009922 chr21 48129895 626843 0.013023984365642186 0.1550175746940156 chr22 51304566 1352748 0.02636700990707143 0.1804456133124292 chrMT 16571 9790 0.5907911411502021 0.8871690079990936 chrX 155270560 3236742 0.020845819065764947 0.1722700851557122 chrY 59373566 216910 0.0036533092858192146 0.15071268302645024