BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525147.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 = 1,806,937 number of mapped reads = 1,626,884 (90.04%) number of supplementary alignments = 38,953 (2.16%) number of secondary alignments = 0 number of mapped bases = 124,840,845 bp number of sequenced bases = 124,792,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,655 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1676 >>>>>>> ACTG content number of A's = 33,401,578 bp (26.77%) number of C's = 23,727,584 bp (19.01%) number of T's = 39,141,976 bp (31.37%) number of G's = 28,516,084 bp (22.85%) number of N's = 4,934 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 945,941 number of insertions = 12,182 mapped reads with insertion percentage = 0.74% number of deletions = 28,300 mapped reads with deletion percentage = 1.72% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.4351X There is a 3.51% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11844874 0.04752194378685219 0.75236432873493 chr2 243199373 10428370 0.04287992140506053 0.6164319957094797 chr3 198022430 7830292 0.03954244981237731 0.22431329471577366 chr4 191154276 8030262 0.04200932444744265 0.2424505000672404 chr5 180915260 7422236 0.04102603616742999 0.22947085194649547 chr6 171115067 7070632 0.04132092003330133 0.26659851168199816 chr7 159138663 6774050 0.04256696564052445 0.6400566839421888 chr8 146364022 6294478 0.04300563700005456 0.548528524262728 chr9 141213431 5057638 0.035815559215468674 0.39139525459652236 chr10 135534747 5698734 0.04204629533118913 0.4718498761767077 chr11 135006516 6867865 0.05087061871887724 0.482585071234915 chr12 133851895 5436346 0.0406146360497922 0.22729256020548624 chr13 115169878 4584009 0.039802152087024006 0.22410119271162507 chr14 107349540 3670269 0.034189890333950194 0.2456573008458291 chr15 102531392 3331474 0.0324922341832636 0.19880515879465707 chr16 90354753 2702347 0.029908188670495287 0.2204374249074513 chr17 81195210 3584327 0.04414456222232814 0.2812228094789442 chr18 78077248 3363676 0.04308138524554554 0.7037047106163857 chr19 59128983 2268190 0.038360037411771485 0.5702370881161987 chr20 63025520 2406100 0.03817659893960415 0.2294694153920946 chr21 48129895 1615490 0.033565209315333015 0.22201579230382795 chr22 51304566 1222890 0.023835890162290818 0.16912063069133423 chrMT 16571 6616 0.39925170478546856 1.0013132021137316 chrX 155270560 7047556 0.045388874748696725 0.332063425298516 chrY 59373566 282124 0.004751676865762114 0.1191156484455836