BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173928.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,037,652 number of mapped reads = 3,952,732 (97.9%) number of supplementary alignments = 569,817 (14.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,973,780 number of mapped paired reads (second in pair) = 1,978,952 number of mapped paired reads (both in pair) = 3,898,272 number of mapped paired reads (singletons) = 54,460 number of mapped bases = 447,365,278 bp number of sequenced bases = 447,065,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,219,122 duplication rate = 64.98% >>>>>>> Insert size mean insert size = 1,050,706.083 std insert size = 9,539,879.9386 median insert size = 152 >>>>>>> Mapping quality mean mapping quality = 52.3794 >>>>>>> ACTG content number of A's = 133,186,396 bp (29.79%) number of C's = 89,159,474 bp (19.94%) number of T's = 132,052,044 bp (29.54%) number of G's = 92,664,088 bp (20.73%) number of N's = 3,847 bp (0%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 3,773,656 number of insertions = 50,762 mapped reads with insertion percentage = 1.23% number of deletions = 123,663 mapped reads with deletion percentage = 3.06% homopolymer indels = 41.4% >>>>>>> Coverage mean coverageData = 0.1445X std coverageData = 2.8048X There is a 3.09% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 1.73% of reference with a coverageData >= 3X There is a 1.4% of reference with a coverageData >= 4X There is a 1.05% of reference with a coverageData >= 5X There is a 0.87% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 36698091 0.14723369936959957 1.511080447222035 chr2 243199373 38953838 0.16017244419458268 8.873932367914804 chr3 198022430 30938348 0.1562365839061767 1.208187698488664 chr4 191154276 30638919 0.16028372287104894 1.4724562136165675 chr5 180915260 27766056 0.15347547796686692 1.1923945382437453 chr6 171115067 24166115 0.14122727719821423 1.22050516793881 chr7 159138663 23782573 0.14944560015563282 1.425078117938873 chr8 146364022 21460818 0.1466263205038189 1.6378997571985396 chr9 141213431 19314241 0.1367733994084458 1.4520298451428821 chr10 135534747 21786955 0.16074811428245778 1.7060825507668205 chr11 135006516 19957927 0.1478293610658022 1.1896686562173795 chr12 133851895 21202312 0.15840128374723422 1.2389168671536461 chr13 115169878 15855019 0.1376663696735009 1.1487846029223696 chr14 107349540 14631171 0.1362946781141307 1.1233039655606687 chr15 102531392 14303493 0.13950354833766423 1.1406926485227473 chr16 90354753 13456015 0.1489242630102702 1.3222022416618124 chr17 81195210 12726482 0.15673931996727394 1.2463963118195533 chr18 78077248 11493562 0.14720757063568635 1.8777099361683827 chr19 59128983 9445790 0.15974890012906193 1.4065047015368894 chr20 63025520 10197769 0.16180380582341883 1.2586111445775128 chr21 48129895 6269174 0.1302553018243651 1.33218706113108 chr22 51304566 5978061 0.11652103245547385 1.1428563595275418 chrMT 16571 930531 56.15418502202643 49.77318407714644 chrX 155270560 11805007 0.07602862384215012 0.8234287144174546 chrY 59373566 3607011 0.06075112618298857 1.032494108711709