BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617372.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,580,656 (92.44%) number of supplementary alignments = 85,471 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,920,260 number of mapped paired reads (second in pair) = 14,660,396 number of mapped paired reads (both in pair) = 28,884,774 number of mapped paired reads (singletons) = 695,882 number of mapped bases = 2,892,261,748 bp number of sequenced bases = 2,891,413,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,546,519 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 57,680.3601 std insert size = 2,294,683.6022 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.3459 >>>>>>> ACTG content number of A's = 878,187,872 bp (30.37%) number of C's = 572,621,545 bp (19.8%) number of T's = 864,823,609 bp (29.91%) number of G's = 575,136,896 bp (19.89%) number of N's = 644,054 bp (0.02%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 35,686,507 number of insertions = 294,202 mapped reads with insertion percentage = 0.96% number of deletions = 353,697 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.15% >>>>>>> Coverage mean coverageData = 0.9343X std coverageData = 9.6064X There is a 52.06% of reference with a coverageData >= 1X There is a 23.26% of reference with a coverageData >= 2X There is a 8.87% of reference with a coverageData >= 3X There is a 3.1% of reference with a coverageData >= 4X There is a 1.06% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 187542649 0.7524260049887699 19.705031842710035 chr2 243199373 285728085 1.1748717995255686 8.586811491873268 chr3 198022430 230880196 1.1659295161664263 1.4672113340390294 chr4 191154276 158793687 0.8307095730361794 8.949045974471408 chr5 180915260 181970561 1.0058331231981206 1.4496639186211926 chr6 171115067 135686766 0.7929562742712774 3.6368086355280798 chr7 159138663 234999124 1.4766940953877437 10.625477716982541 chr8 146364022 121822222 0.8323235473810634 7.411018060647865 chr9 141213431 121497603 0.8603827705312251 14.404050544107186 chr10 135534747 121950768 0.8997749337297247 19.90892769298933 chr11 135006516 155160236 1.1492796095856588 5.45035367296635 chr12 133851895 127713498 0.9541403803061586 1.3968640349133628 chr13 115169878 126404005 1.0975439689186786 1.2954357065803275 chr14 107349540 83503218 0.7778628394681524 1.3580699599845898 chr15 102531392 64913657 0.6331100722791319 1.0247811644772324 chr16 90354753 72729473 0.8049324533043657 7.811963395002679 chr17 81195210 89342552 1.100342643365292 7.012418140675187 chr18 78077248 52400657 0.6711386267097939 14.864794565608163 chr19 59128983 53201515 0.8997535946119689 9.574514181557435 chr20 63025520 82251616 1.305052556488229 2.358185764201296 chr21 48129895 45952890 0.9547681331945561 3.1670152171603476 chr22 51304566 25419776 0.49546810317038836 0.9066685047058298 chrMT 16571 1941935 117.18876350250437 22.129566608196484 chrX 155270560 120689646 0.777286086943977 2.9887584685077213 chrY 59373566 9765413 0.1644740859930832 8.150716133092201