BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173926.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 = 3,195,206 number of mapped reads = 3,123,841 (97.77%) number of supplementary alignments = 400,521 (12.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,562,907 number of mapped paired reads (second in pair) = 1,560,934 number of mapped paired reads (both in pair) = 3,080,908 number of mapped paired reads (singletons) = 42,933 number of mapped bases = 350,450,768 bp number of sequenced bases = 350,193,912 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,442,686 duplication rate = 61.6% >>>>>>> Insert size mean insert size = 812,970.4387 std insert size = 8,343,962.9157 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 52.5612 >>>>>>> ACTG content number of A's = 105,235,866 bp (30.05%) number of C's = 69,070,612 bp (19.72%) number of T's = 104,205,887 bp (29.76%) number of G's = 71,679,011 bp (20.47%) number of N's = 2,536 bp (0%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,976,598 number of insertions = 39,297 mapped reads with insertion percentage = 1.21% number of deletions = 107,784 mapped reads with deletion percentage = 3.36% homopolymer indels = 40.58% >>>>>>> Coverage mean coverageData = 0.1132X std coverageData = 2.2417X There is a 2.58% of reference with a coverageData >= 1X There is a 1.84% of reference with a coverageData >= 2X There is a 1.31% of reference with a coverageData >= 3X There is a 1.05% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.66% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 27724510 0.11123145807528399 1.1571044164144444 chr2 243199373 31890763 0.1311301201422094 6.9527870587852245 chr3 198022430 24089739 0.12165156745122258 1.0546645202812008 chr4 191154276 23505148 0.1229642804328374 1.298999097101396 chr5 180915260 21777186 0.12037230026919786 1.0508170943452482 chr6 171115067 20969555 0.12254651427042365 1.1415743166328616 chr7 159138663 19464815 0.12231355117015152 1.2031717171158924 chr8 146364022 17895215 0.1222651219573619 1.4528434106349075 chr9 141213431 14856885 0.10520872479898885 1.1197550137407923 chr10 135534747 16929364 0.12490792490282954 1.453637783836386 chr11 135006516 15752467 0.1166793090194254 1.0343587933455496 chr12 133851895 16163978 0.1207601730255668 1.067531013873372 chr13 115169878 11444349 0.09936928994576169 0.9542399469862821 chr14 107349540 11133657 0.10371406342309432 0.9749746548724452 chr15 102531392 10395457 0.10138804123521507 0.961581854586673 chr16 90354753 10824316 0.11979797011895987 1.1524999900631572 chr17 81195210 9600912 0.11824480779100147 1.0960597394181848 chr18 78077248 9342306 0.1196546527869425 1.3047972071495773 chr19 59128983 6411976 0.10844049186504696 1.0309089749879683 chr20 63025520 7249014 0.11501712322246607 1.0300027367096831 chr21 48129895 4853895 0.10084989796881959 1.0467747692748484 chr22 51304566 4323615 0.084273493318314 0.9379160921221972 chrMT 16571 1358188 81.96174038983767 69.62019518447818 chrX 155270560 9771083 0.06292939885062564 0.754324381650115 chrY 59373566 2722375 0.04585163370514077 0.8339079597800103