BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716719.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 = 535,532 number of mapped reads = 488,905 (91.29%) number of supplementary alignments = 2,440 (0.46%) number of secondary alignments = 0 number of mapped bases = 28,757,803 bp number of sequenced bases = 28,749,117 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,198 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7966 >>>>>>> ACTG content number of A's = 7,288,976 bp (25.35%) number of C's = 5,594,656 bp (19.46%) number of T's = 9,032,824 bp (31.42%) number of G's = 6,832,362 bp (23.77%) number of N's = 299 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 140,933 number of insertions = 2,393 mapped reads with insertion percentage = 0.49% number of deletions = 5,446 mapped reads with deletion percentage = 1.1% homopolymer indels = 39.65% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 0.1175X There is a 0.89% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2360083 0.009468714623583625 0.1679985604345819 chr2 243199373 2823734 0.011610778289300934 0.13733018194075636 chr3 198022430 1954876 0.00987199278384777 0.10284290979395025 chr4 191154276 1619562 0.008472538694347597 0.09732290711192605 chr5 180915260 1540640 0.00851581010910854 0.09467516775303396 chr6 171115067 1615314 0.009439928513133211 0.10354004412667511 chr7 159138663 1380749 0.008676389344806799 0.15601808806088174 chr8 146364022 2477653 0.016928019373504233 0.15096451256214422 chr9 141213431 1201280 0.00850683955126053 0.09978407601194945 chr10 135534747 1361145 0.01004277523017769 0.13639824915330173 chr11 135006516 1082768 0.008020116599409172 0.09838697344567014 chr12 133851895 1367958 0.010219937491359386 0.10643852656257759 chr13 115169878 694286 0.006028364465229355 0.0795742744383552 chr14 107349540 926632 0.00863191402590081 0.09593751266238075 chr15 102531392 676321 0.006596233473549252 0.08415246886480987 chr16 90354753 858123 0.009497264632000046 0.10206135342689539 chr17 81195210 1183119 0.014571290597068472 0.1256032901143824 chr18 78077248 665785 0.008527260079658545 0.13111178992807768 chr19 59128983 556019 0.009403493376505393 0.13661623430235567 chr20 63025520 624569 0.009909779403644747 0.10301589590352832 chr21 48129895 303255 0.0063007617199248 0.08297244891685358 chr22 51304566 410580 0.008002796476243459 0.09210143663538252 chrMT 16571 3424 0.20662603343189911 0.42806840573215715 chrX 155270560 1007108 0.006486149080675693 0.0863044549940999 chrY 59373566 62820 0.0010580466061277168 0.041282201179986454