BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525262.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 = 1,210,974 number of mapped reads = 1,102,528 (91.04%) number of supplementary alignments = 4,253 (0.35%) number of secondary alignments = 0 number of mapped bases = 63,367,510 bp number of sequenced bases = 63,346,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,277 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8637 >>>>>>> ACTG content number of A's = 16,059,110 bp (25.35%) number of C's = 11,411,558 bp (18.01%) number of T's = 20,890,956 bp (32.98%) number of G's = 14,984,097 bp (23.65%) number of N's = 1,200 bp (0%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 321,675 number of insertions = 4,156 mapped reads with insertion percentage = 0.38% number of deletions = 13,103 mapped reads with deletion percentage = 1.18% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 0.2191X There is a 1.89% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6800680 0.027284505742515282 0.37969925712652247 chr2 243199373 5349768 0.02199745802798595 0.2919464560818779 chr3 198022430 3944435 0.019919132393234444 0.15054764394363326 chr4 191154276 3565384 0.01865186630719158 0.1488637649237166 chr5 180915260 2855776 0.01578515820058518 0.13396164870767122 chr6 171115067 3156286 0.01844540083661949 0.1628940087501569 chr7 159138663 4709975 0.02959667318557276 0.3610260011355117 chr8 146364022 4022207 0.02748084498525191 0.22623602217747474 chr9 141213431 1905726 0.013495359375554015 0.15079885754763478 chr10 135534747 4230303 0.03121194449125286 0.23373286515544664 chr11 135006516 2885602 0.02137379798764676 0.18553895873763027 chr12 133851895 2832454 0.021161104966052217 0.15518035606844696 chr13 115169878 1969873 0.017104064310982426 0.1404944760968736 chr14 107349540 1446759 0.013477086161710615 0.12782288203662664 chr15 102531392 1750119 0.017069104065221313 0.1427890326982905 chr16 90354753 1665880 0.018437104243979284 0.15642528835448546 chr17 81195210 1134394 0.013971193620904484 0.12829866959912073 chr18 78077248 1344083 0.01721478451699527 0.29008064721024845 chr19 59128983 1229187 0.020788231720474542 0.26245009002471165 chr20 63025520 1171975 0.018595245227647467 0.1474004861175075 chr21 48129895 876494 0.018211010017786244 0.1479921401347836 chr22 51304566 689547 0.01344026572605643 0.12267644733826856 chrMT 16571 2243 0.13535694888660912 0.38852299221758435 chrX 155270560 3640795 0.023448070258779256 0.1725839355129482 chrY 59373566 187565 0.0031590657701105573 0.09023204244975566