BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094091.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 784,100 number of mapped reads = 746,368 (95.19%) number of supplementary alignments = 72,301 (9.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 375,014 number of mapped paired reads (second in pair) = 371,354 number of mapped paired reads (both in pair) = 740,356 number of mapped paired reads (singletons) = 6,012 number of mapped bases = 92,111,435 bp number of sequenced bases = 90,475,160 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 742,966 duplication rate = 56.4% >>>>>>> Insert size mean insert size = 2,412,893.4376 std insert size = 13,614,771.4739 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 41.5843 >>>>>>> ACTG content number of A's = 25,745,696 bp (28.46%) number of C's = 19,712,070 bp (21.79%) number of T's = 24,186,554 bp (26.73%) number of G's = 20,829,850 bp (23.02%) number of N's = 990 bp (0%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.0346 number of mismatches = 2,999,615 number of insertions = 62,637 mapped reads with insertion percentage = 8.26% number of deletions = 232,967 mapped reads with deletion percentage = 30.21% homopolymer indels = 28% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 5.2891X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 2049532 0.008222775902331654 2.955032173034724 chr2 243199373 4013881 0.016504487451947502 4.823553540542726 chr3 198022430 1545342 0.007803873530892434 2.091865159232377 chr4 191154276 4023472 0.021048297135660202 5.789751087201392 chr5 180915260 1524528 0.008426751839507623 3.3544791503167506 chr6 171115067 1992120 0.011641990591044796 3.4981399667652564 chr7 159138663 1915708 0.012037979733435362 3.1717781591568897 chr8 146364022 1706136 0.011656799100533053 2.908787638266449 chr9 141213431 1558697 0.011037880667314145 3.961282243580721 chr10 135534747 1343829 0.009915014634586657 2.3564937757124587 chr11 135006516 2505796 0.01856055599568246 4.433402249907278 chr12 133851895 2197200 0.016415157962462915 3.373572203631176 chr13 115169878 1553399 0.013487893075652993 2.9727725340964497 chr14 107349540 357249 0.0033279043394130983 1.2336463292046034 chr15 102531392 854941 0.008338334078210895 1.990813147311696 chr16 90354753 277905 0.0030757098079832058 0.815296361823234 chr17 81195210 628170 0.0077365401234875805 1.8997003261905059 chr18 78077248 498289 0.006382000041804752 1.8708854376996564 chr19 59128983 168663 0.002852459004748991 0.8063157976769437 chr20 63025520 291245 0.004621064610018291 1.2586791994108144 chr21 48129895 338276 0.007028396799951465 2.370930721621906 chr22 51304566 127546 0.0024860555296384343 0.835611875672007 chrMT 16571 509560 30.75010560617947 154.3216232478939 chrX 155270560 58285861 0.37538256447326523 18.426563798565184 chrY 59373566 1844090 0.03105910802123625 5.141117557456719