BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716322.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 = 1,668,425 number of mapped reads = 1,517,849 (90.97%) number of supplementary alignments = 7,146 (0.43%) number of secondary alignments = 0 number of mapped bases = 88,379,449 bp number of sequenced bases = 88,353,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,342 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7953 >>>>>>> ACTG content number of A's = 22,742,067 bp (25.74%) number of C's = 17,268,314 bp (19.54%) number of T's = 27,637,478 bp (31.28%) number of G's = 20,703,510 bp (23.43%) number of N's = 2,541 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 435,426 number of insertions = 5,632 mapped reads with insertion percentage = 0.37% number of deletions = 16,357 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2727X There is a 2.57% of reference with a coverageData >= 1X There is a 0.21% 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 10044006 0.040296814345750415 0.5213194661998094 chr2 243199373 7653110 0.03146846106383671 0.33995281659148857 chr3 198022430 8035040 0.04057641349012837 0.22056957237177655 chr4 191154276 4127719 0.021593652448559403 0.1681769498626462 chr5 180915260 3895009 0.021529466336891647 0.1620490243043174 chr6 171115067 6345220 0.037081597262267965 0.2875773519305865 chr7 159138663 5106706 0.0320896625856408 0.33402022024857486 chr8 146364022 5837301 0.03988207566474226 0.24865205076737681 chr9 141213431 3321754 0.02352293246100649 0.2188952593009202 chr10 135534747 4544270 0.03352845008815341 0.28375326693791614 chr11 135006516 2988494 0.022135924165319548 0.21168827153744565 chr12 133851895 3916451 0.029259585753343274 0.19157546180981141 chr13 115169878 2029113 0.017618434917505078 0.14448284429341038 chr14 107349540 1930266 0.01798112968159901 0.15936207673261882 chr15 102531392 2617635 0.02553008350847319 0.1760620862706031 chr16 90354753 1885459 0.020867291840197935 0.17520953666228542 chr17 81195210 1940601 0.023900436983905825 0.17465220641324514 chr18 78077248 1727499 0.022125510878662116 0.3874019327866128 chr19 59128983 1886988 0.03191308059534865 0.3521975350039286 chr20 63025520 1365131 0.021659972024030902 0.16250143420863122 chr21 48129895 825621 0.017154016230453026 0.15342985756013441 chr22 51304566 1428731 0.027848028185249632 0.18254380579855467 chrMT 16571 1730 0.10439925170478546 0.34839643989051927 chrX 155270560 4713391 0.030355986350535477 0.21460571434934123 chrY 59373566 212204 0.003574048424175836 0.08908725442510913