BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174030.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 = 2,493,554 number of mapped reads = 2,429,013 (97.41%) number of supplementary alignments = 252,717 (10.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,215,842 number of mapped paired reads (second in pair) = 1,213,171 number of mapped paired reads (both in pair) = 2,386,396 number of mapped paired reads (singletons) = 42,617 number of mapped bases = 286,003,220 bp number of sequenced bases = 285,824,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,812,235 duplication rate = 62.16% >>>>>>> Insert size mean insert size = 748,563.6873 std insert size = 8,059,455.6336 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.5551 >>>>>>> ACTG content number of A's = 86,406,811 bp (30.23%) number of C's = 55,557,861 bp (19.44%) number of T's = 86,287,425 bp (30.19%) number of G's = 57,569,720 bp (20.14%) number of N's = 3,021 bp (0%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 2,965,344 number of insertions = 30,940 mapped reads with insertion percentage = 1.23% number of deletions = 72,221 mapped reads with deletion percentage = 2.9% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0924X std coverageData = 1.5297X There is a 2.18% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% 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 0.01% 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 26509345 0.10635618436433103 1.3953022905654744 chr2 243199373 25152062 0.10342157419953546 4.0628164369750275 chr3 198022430 21167187 0.10689287572119986 0.9021263712339067 chr4 191154276 18375642 0.0961299029481297 0.9566274989916872 chr5 180915260 19765581 0.10925325481111986 0.9171835602455856 chr6 171115067 16450143 0.09613497682235078 0.875258820787649 chr7 159138663 20689694 0.13001048023131878 1.6494662898264383 chr8 146364022 12127507 0.08285852516405978 0.9405055189792646 chr9 141213431 11798814 0.08355305806570199 0.9238175438692071 chr10 135534747 12397281 0.09146939271595055 1.7167865921711671 chr11 135006516 14099313 0.10443431485929168 0.8958824774413121 chr12 133851895 9781212 0.07307488623900318 0.7358470496663531 chr13 115169878 9429476 0.08187449846912229 0.7914333339860464 chr14 107349540 7199001 0.0670613120466096 0.7098772574291093 chr15 102531392 6981328 0.0680896637002646 0.7169865885542983 chr16 90354753 11863714 0.1313014933481142 1.3794390772979204 chr17 81195210 6829843 0.08411632902975434 0.8406285633316606 chr18 78077248 4437363 0.056832984174852066 1.2034047807289525 chr19 59128983 5021800 0.08492958520866155 1.2999684964535718 chr20 63025520 8462843 0.1342764486512765 1.0070527102110798 chr21 48129895 4412780 0.09168480421575821 0.8432024985567358 chr22 51304566 2561398 0.04992534192765611 0.5887747001129651 chrMT 16571 695374 41.963309395932654 32.74047818971969 chrX 155270560 9356996 0.060262524975758444 0.6672493806226388 chrY 59373566 437523 0.0073689863937092814 0.3417763130895886