BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819054.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,703,161 number of mapped reads = 1,559,186 (91.55%) number of supplementary alignments = 6,465 (0.38%) number of secondary alignments = 0 number of mapped bases = 89,541,173 bp number of sequenced bases = 89,518,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,977 duplication rate = 2.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5873 >>>>>>> ACTG content number of A's = 22,634,430 bp (25.28%) number of C's = 18,009,087 bp (20.12%) number of T's = 27,448,613 bp (30.66%) number of G's = 21,424,671 bp (23.93%) number of N's = 1,883 bp (0%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 430,225 number of insertions = 5,051 mapped reads with insertion percentage = 0.32% number of deletions = 13,156 mapped reads with deletion percentage = 0.84% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2294X There is a 2.59% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 9975662 0.04002261643312014 0.33649584288135037 chr2 243199373 7463431 0.030688528954390025 0.26754686409228323 chr3 198022430 6052440 0.030564416364348222 0.19169181868163152 chr4 191154276 6095692 0.03188886028372182 0.20840311143077148 chr5 180915260 4830925 0.026702694952321877 0.17973531496568754 chr6 171115067 4795932 0.028027526062330912 0.19166190591482757 chr7 159138663 4721248 0.029667510779577178 0.22085543219673592 chr8 146364022 5368140 0.03667663628429123 0.23423564911629363 chr9 141213431 3567058 0.025260047679175786 0.23956761476667673 chr10 135534747 4545896 0.033540447011717225 0.2531872359932237 chr11 135006516 3233069 0.023947503393095485 0.22432872782082613 chr12 133851895 4054103 0.030287976124656286 0.19236690165837725 chr13 115169878 1569277 0.013625758985348582 0.1260986273909277 chr14 107349540 2260445 0.021056867127702644 0.16863474583836746 chr15 102531392 2814679 0.0274518754217245 0.1810941337585267 chr16 90354753 2782698 0.030797472270219145 0.20516172022931028 chr17 81195210 1969437 0.024255581086618287 0.17557537762608982 chr18 78077248 2256516 0.02890106987377424 0.4057361337384433 chr19 59128983 1433349 0.024241056200814414 0.2540840874066029 chr20 63025520 1993046 0.03162284103328303 0.2001789848042176 chr21 48129895 1207540 0.025089188330870035 0.19105824460311557 chr22 51304566 1095730 0.021357358329471103 0.16030493011543587 chrMT 16571 15950 0.9625248928851609 1.0521566200384753 chrX 155270560 5179436 0.0333574890178795 0.22131780419451969 chrY 59373566 259474 0.004370193968137269 0.10020091029173796