BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240057.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,447,151 number of mapped reads = 1,148,607 (79.37%) number of supplementary alignments = 6,617 (0.46%) number of secondary alignments = 0 number of mapped bases = 72,808,022 bp number of sequenced bases = 72,764,014 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,887 duplication rate = 8.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1905 >>>>>>> ACTG content number of A's = 20,064,201 bp (27.57%) number of C's = 13,052,749 bp (17.94%) number of T's = 23,492,778 bp (32.29%) number of G's = 16,103,885 bp (22.13%) number of N's = 50,401 bp (0.07%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 739,588 number of insertions = 5,390 mapped reads with insertion percentage = 0.47% number of deletions = 25,653 mapped reads with deletion percentage = 2.21% homopolymer indels = 49.42% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 0.2686X There is a 1.51% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 5738838 0.02302436791120372 0.36846842976074246 chr2 243199373 7122174 0.029285330435453054 0.30769110273262773 chr3 198022430 4990860 0.025203508511636788 0.23132124505559032 chr4 191154276 4810225 0.025164098343266984 0.2362130675045465 chr5 180915260 4341025 0.023994797343242356 0.22652202485675682 chr6 171115067 4209803 0.024602176031640745 0.2502950482484696 chr7 159138663 4470195 0.028089936887304375 0.3946580808799321 chr8 146364022 4307182 0.029427874016744363 0.3192022130655013 chr9 141213431 2764432 0.019576268209218713 0.2363248464283776 chr10 135534747 3197317 0.02359038601370614 0.24739281130854615 chr11 135006516 3327304 0.024645506739837654 0.26353734154528197 chr12 133851895 3221362 0.024066614820806236 0.22590568479959558 chr13 115169878 1937292 0.016821169160220868 0.1889641603915546 chr14 107349540 2432809 0.02266250046343934 0.22801273782022782 chr15 102531392 1820789 0.01775835638708582 0.19563455679901254 chr16 90354753 1964228 0.021739066676437043 0.21456489999619058 chr17 81195210 1858486 0.022889108852603497 0.22520956852550364 chr18 78077248 1711642 0.02192241714257142 0.3577419598715069 chr19 59128983 1245915 0.021071138666464127 0.2783126392711615 chr20 63025520 1456971 0.023117159525220896 0.2284331905559954 chr21 48129895 1166494 0.02423637117845364 0.23294727978672572 chr22 51304566 666055 0.01298237275801144 0.16094326103663653 chrMT 16571 49727 3.000844849435761 3.8563459108301914 chrX 155270560 3816352 0.024578722457109705 0.23486964898542148 chrY 59373566 180545 0.00304083133561491 0.07917925705847964