BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927043.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 34,262,418 number of mapped reads = 33,613,808 (98.11%) number of supplementary alignments = 361,392 (1.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,881,187 number of mapped paired reads (second in pair) = 16,732,621 number of mapped paired reads (both in pair) = 33,269,830 number of mapped paired reads (singletons) = 343,978 number of mapped bases = 3,136,864,084 bp number of sequenced bases = 3,134,520,691 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,696,021 duplication rate = 6.28% >>>>>>> Insert size mean insert size = 135,558.5299 std insert size = 3,621,875.3432 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 53.3024 >>>>>>> ACTG content number of A's = 899,297,291 bp (28.69%) number of C's = 618,104,104 bp (19.72%) number of T's = 912,684,100 bp (29.12%) number of G's = 703,981,786 bp (22.46%) number of N's = 453,410 bp (0.01%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 33,017,428 number of insertions = 508,682 mapped reads with insertion percentage = 1.49% number of deletions = 1,651,425 mapped reads with deletion percentage = 4.79% homopolymer indels = 52.76% >>>>>>> Coverage mean coverageData = 1.0133X std coverageData = 3.6136X There is a 37.21% of reference with a coverageData >= 1X There is a 21.77% of reference with a coverageData >= 2X There is a 13.34% of reference with a coverageData >= 3X There is a 8.59% of reference with a coverageData >= 4X There is a 5.69% of reference with a coverageData >= 5X There is a 3.86% of reference with a coverageData >= 6X There is a 2.66% of reference with a coverageData >= 7X There is a 1.86% of reference with a coverageData >= 8X There is a 1.32% of reference with a coverageData >= 9X There is a 0.94% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% 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 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 256659537 1.0297247644570562 4.73872451639512 chr2 243199373 272995590 1.1225176555039884 6.764852773075427 chr3 198022430 213198007 1.0766356467800138 2.0448714109816764 chr4 191154276 190887685 0.9986053620898336 2.6903757241969566 chr5 180915260 189992748 1.0501753583418005 1.9970582229551863 chr6 171115067 181716479 1.0619548715718878 2.0351177360349126 chr7 159138663 161579719 1.0153391762503372 2.589897995527705 chr8 146364022 161615352 1.1042013589924442 2.473837996337477 chr9 141213431 138715492 0.9823108964755626 4.929172067727195 chr10 135534747 151740116 1.119566158189678 5.430775531178627 chr11 135006516 147702620 1.0940406757848635 3.4112710846559784 chr12 133851895 140943180 1.0529785924958328 2.0351446856390734 chr13 115169878 94975856 0.8246588226827851 1.7715366571086648 chr14 107349540 93547387 0.8714279260069488 1.9152921566272887 chr15 102531392 94220049 0.9189385529848263 2.0067869562500946 chr16 90354753 97169074 1.0754174049925187 5.037972585795233 chr17 81195210 79353400 0.977316272721014 2.811450260349944 chr18 78077248 84758449 1.0855716763992502 4.840497434554464 chr19 59128983 50836635 0.859758318522069 2.945715599296264 chr20 63025520 72948293 1.157440557412299 2.3198577462577497 chr21 48129895 40000002 0.8310843395773043 2.5872809975439877 chr22 51304566 39029460 0.7607404767832945 1.8952515317333338 chrMT 16571 71974 4.343370949248688 3.920915511932419 chrX 155270560 177526438 1.1433361095625596 2.4848327682555396 chrY 59373566 4680542 0.07883208497195536 1.8807667476493666