BamQC report ----------------------------------- >>>>>>> Input bam file = SRR620533.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.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 = 14,641,324 number of mapped reads = 7,440,598 (50.82%) number of supplementary alignments = 240 (0%) number of secondary alignments = 0 number of mapped bases = 315,016,612 bp number of sequenced bases = 314,940,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,203,458 duplication rate = 8.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8356 >>>>>>> ACTG content number of A's = 80,399,460 bp (25.53%) number of C's = 53,363,349 bp (16.94%) number of T's = 101,597,642 bp (32.26%) number of G's = 79,415,412 bp (25.22%) number of N's = 165,079 bp (0.05%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 2,110,507 number of insertions = 21,207 mapped reads with insertion percentage = 0.28% number of deletions = 52,838 mapped reads with deletion percentage = 0.7% homopolymer indels = 41.82% >>>>>>> Coverage mean coverageData = 0.1018X std coverageData = 1.393X There is a 7.28% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 25608065 0.102740225469689 2.5582676662726 chr2 243199373 26166488 0.10759274449280755 0.8778327590380168 chr3 198022430 21049276 0.10629743307361697 0.6202998976224926 chr4 191154276 18884279 0.09879077463064441 0.8210407090600473 chr5 180915260 17883566 0.09885051155994248 0.5624280914675435 chr6 171115067 18705316 0.10931425460038537 0.6593789020530555 chr7 159138663 17284044 0.10860996111296976 1.5381580086754427 chr8 146364022 17710023 0.12099983833458744 1.4997361803612312 chr9 141213431 13820288 0.09786808451669161 0.9078996186654558 chr10 135534747 15410625 0.11370239249422881 1.0750350666464172 chr11 135006516 15333258 0.11357420704049573 3.645300833027625 chr12 133851895 14679234 0.10966773387855286 0.6546632440510122 chr13 115169878 9772516 0.08485305506705494 0.5173116561686374 chr14 107349540 8994987 0.08379157470073928 0.5406424256384643 chr15 102531392 8575517 0.08363796523897774 0.48711409266808753 chr16 90354753 8464122 0.09367655512267296 0.572004633980937 chr17 81195210 7313759 0.09007623725586768 0.6887850523036338 chr18 78077248 8140572 0.10426304984519946 2.2217056378184945 chr19 59128983 5955839 0.10072622084502958 1.6495172811240821 chr20 63025520 6232624 0.09889048118920717 0.6795592438497088 chr21 48129895 5546770 0.11524583629363828 0.6555003041668789 chr22 51304566 2989187 0.05826356663849373 0.3788422096407006 chrMT 16571 123490 7.452175487297085 12.064595498023944 chrX 155270560 19238528 0.12390325635458518 1.2691500288016344 chrY 59373566 1134239 0.019103434009673598 0.3886301860063439