BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927022.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 = 8,853,220 number of mapped reads = 8,678,980 (98.03%) number of supplementary alignments = 263,846 (2.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,349,169 number of mapped paired reads (second in pair) = 4,329,811 number of mapped paired reads (both in pair) = 8,569,154 number of mapped paired reads (singletons) = 109,826 number of mapped bases = 797,240,146 bp number of sequenced bases = 796,626,846 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 432,834 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 355,254.1586 std insert size = 5,867,915.6006 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 52.2902 >>>>>>> ACTG content number of A's = 227,922,227 bp (28.61%) number of C's = 155,547,617 bp (19.53%) number of T's = 232,402,007 bp (29.17%) number of G's = 180,602,223 bp (22.67%) number of N's = 152,772 bp (0.02%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 7,599,882 number of insertions = 140,359 mapped reads with insertion percentage = 1.59% number of deletions = 415,679 mapped reads with deletion percentage = 4.67% homopolymer indels = 51.74% >>>>>>> Coverage mean coverageData = 0.2575X std coverageData = 1.3615X There is a 16.63% of reference with a coverageData >= 1X There is a 5.56% of reference with a coverageData >= 2X There is a 1.85% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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% 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 64897790 0.2603716281212395 1.9091772839269923 chr2 243199373 69747531 0.28679157408847433 1.7868235679104725 chr3 198022430 53533983 0.27034302629252654 0.7247656057881733 chr4 191154276 49404762 0.25845491418669597 0.9602670048029661 chr5 180915260 48938601 0.27050565552071176 0.6994091178803419 chr6 171115067 45900858 0.2682455660085152 0.7859180208015455 chr7 159138663 41915390 0.26338910488395895 0.963492591377995 chr8 146364022 40433475 0.2762528280344742 0.8194292354003189 chr9 141213431 33347743 0.2361513544699583 1.520423044540292 chr10 135534747 40334958 0.29759865195306706 3.389579446078763 chr11 135006516 37729400 0.27946354826310754 1.514024702590045 chr12 133851895 36040485 0.2692564419801453 0.7068586984385185 chr13 115169878 24062695 0.20893219145374106 0.6115141654098795 chr14 107349540 23875655 0.22241040809303886 0.6518784974583435 chr15 102531392 22551832 0.2199505103763733 0.6422744060665245 chr16 90354753 25246974 0.27942054138535466 1.9424010415302981 chr17 81195210 19918407 0.24531504998878628 0.7952453608826299 chr18 78077248 21571531 0.27628446894029873 1.657376205431284 chr19 59128983 12585041 0.2128404779091161 1.2019837801362803 chr20 63025520 17862663 0.2834195259317178 0.7513070357262561 chr21 48129895 10380143 0.21566934646335714 0.8307571296897277 chr22 51304566 9441743 0.1840331911198703 0.6078100513751624 chrMT 16571 75508 4.556635085390139 4.395866349361004 chrX 155270560 45973252 0.29608479546927635 0.8643478086747243 chrY 59373566 1469726 0.024753877845235032 0.8205968130715123