BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975249.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,368,800 number of mapped reads = 4,335,699 (99.24%) number of supplementary alignments = 10,118 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,167,521 number of mapped paired reads (second in pair) = 2,168,178 number of mapped paired reads (both in pair) = 4,325,192 number of mapped paired reads (singletons) = 10,507 number of mapped bases = 399,565,631 bp number of sequenced bases = 399,379,026 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,995 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 55,176.9484 std insert size = 2,252,456.0309 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 52.9231 >>>>>>> ACTG content number of A's = 117,832,145 bp (29.5%) number of C's = 76,968,131 bp (19.27%) number of T's = 119,080,451 bp (29.82%) number of G's = 85,492,346 bp (21.41%) number of N's = 5,953 bp (0%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 2,836,413 number of insertions = 64,966 mapped reads with insertion percentage = 1.48% number of deletions = 117,095 mapped reads with deletion percentage = 2.65% homopolymer indels = 45.34% >>>>>>> Coverage mean coverageData = 0.1291X std coverageData = 1.4381X There is a 8.98% of reference with a coverageData >= 1X There is a 2.53% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 36116513 0.14490039324716467 2.1664539347803067 chr2 243199373 31491565 0.12948867676562636 1.2894036683827428 chr3 198022430 20404158 0.10303963040954502 0.4560146256169414 chr4 191154276 17058950 0.08924179127439451 0.5419045131248783 chr5 180915260 24183798 0.13367472705176997 0.45854683877508545 chr6 171115067 29152228 0.17036622496837173 1.430265543806796 chr7 159138663 21998997 0.13823791519475062 1.7126396033701865 chr8 146364022 20113243 0.1374193106007978 0.5587022684287072 chr9 141213431 13174985 0.09329838462745091 1.0707195224437729 chr10 135534747 18562587 0.13695814107359494 4.28001612671199 chr11 135006516 18245689 0.13514672876974324 0.8701898842857031 chr12 133851895 22769902 0.1701126607135446 0.5398141436912041 chr13 115169878 19128889 0.1660928129141545 0.5290183602996793 chr14 107349540 11843250 0.11032418024334338 0.43250260885155883 chr15 102531392 6705358 0.06539809778453022 0.31492403665647567 chr16 90354753 16168696 0.17894682308522275 2.4548514605562515 chr17 81195210 8381533 0.10322693912608884 1.1119377850353058 chr18 78077248 9476914 0.121378688961988 1.401216493697671 chr19 59128983 10924593 0.1847586825567421 1.0950338483469002 chr20 63025520 8693333 0.13793353866814587 0.4786985870713771 chr21 48129895 3524136 0.07322135234244745 0.35729263589522414 chr22 51304566 2234438 0.043552419876234795 0.25927703147913783 chrMT 16571 16781 1.012672741536419 1.3167530672708296 chrX 155270560 28632883 0.18440638714769883 0.7193570908481839 chrY 59373566 562212 0.009469062377018082 0.25108766041778885