BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716640.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 = 620,632 number of mapped reads = 571,444 (92.07%) number of supplementary alignments = 2,000 (0.32%) number of secondary alignments = 0 number of mapped bases = 32,996,914 bp number of sequenced bases = 32,986,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,828 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3759 >>>>>>> ACTG content number of A's = 8,036,776 bp (24.36%) number of C's = 6,403,117 bp (19.41%) number of T's = 10,423,064 bp (31.6%) number of G's = 8,123,143 bp (24.63%) number of N's = 710 bp (0%) GC percentage = 44.04% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 167,322 number of insertions = 2,381 mapped reads with insertion percentage = 0.41% number of deletions = 6,243 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.0107X std coverageData = 0.1307X There is a 1.01% of reference with a coverageData >= 1X There is a 0.04% 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 2828602 0.011348425085769396 0.1728401720263712 chr2 243199373 2641910 0.010863144782860932 0.16395323008701634 chr3 198022430 1910302 0.009646897071205519 0.10231206751909006 chr4 191154276 2080064 0.010881598065847086 0.1219243687457941 chr5 180915260 1510026 0.008346592763927156 0.09472706782040667 chr6 171115067 1768121 0.010332935789926669 0.11419872928063614 chr7 159138663 1905023 0.011970837030345039 0.1581552057737614 chr8 146364022 1761606 0.012035785679625557 0.16978538237272842 chr9 141213431 1103642 0.007815418067421646 0.10001461065428052 chr10 135534747 1502699 0.01108718637295276 0.14341459524858685 chr11 135006516 1182941 0.00876210300842072 0.10821252130772782 chr12 133851895 1665047 0.012439472747098576 0.11564812604101869 chr13 115169878 1007799 0.008750543262709716 0.09699476608287831 chr14 107349540 1132803 0.010552471859683795 0.10720766576259157 chr15 102531392 1219168 0.01189068027087743 0.11332551857653422 chr16 90354753 1146774 0.012691905648837312 0.12061401302675485 chr17 81195210 1447501 0.01782741863713389 0.1412495296136912 chr18 78077248 610106 0.007814132998130262 0.14082370916974712 chr19 59128983 856387 0.014483371039884112 0.15554841450829937 chr20 63025520 1048465 0.016635562864058876 0.1356807547080886 chr21 48129895 437633 0.009092747864918467 0.1123992966493812 chr22 51304566 315005 0.006139901855908888 0.0812196227403103 chrMT 16571 7000 0.42242471788063485 0.7174876847899813 chrX 155270560 1785061 0.011496454962228512 0.11440901876479531 chrY 59373566 123229 0.0020754859157356325 0.10342228014010499