BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960908.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 79,035,650 number of mapped reads = 74,343,536 (94.06%) number of supplementary alignments = 1,289,385 (1.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 37,242,879 number of mapped paired reads (second in pair) = 37,100,657 number of mapped paired reads (both in pair) = 73,042,722 number of mapped paired reads (singletons) = 1,300,814 number of mapped bases = 6,576,077,050 bp number of sequenced bases = 6,574,234,915 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,915,216 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 159,581.6717 std insert size = 4,160,030.5156 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.4376 >>>>>>> ACTG content number of A's = 1,899,583,535 bp (28.89%) number of C's = 1,358,803,996 bp (20.67%) number of T's = 1,930,895,212 bp (29.37%) number of G's = 1,384,515,119 bp (21.06%) number of N's = 437,053 bp (0.01%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0153 number of mismatches = 98,398,093 number of insertions = 1,049,024 mapped reads with insertion percentage = 1.38% number of deletions = 862,322 mapped reads with deletion percentage = 1.13% homopolymer indels = 37.24% >>>>>>> Coverage mean coverageData = 2.1243X std coverageData = 29.9104X There is a 72.25% of reference with a coverageData >= 1X There is a 51.79% of reference with a coverageData >= 2X There is a 32.92% of reference with a coverageData >= 3X There is a 19.8% of reference with a coverageData >= 4X There is a 11.21% of reference with a coverageData >= 5X There is a 6.17% of reference with a coverageData >= 6X There is a 3.32% of reference with a coverageData >= 7X There is a 1.78% of reference with a coverageData >= 8X There is a 0.97% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 607550179 2.4375071827804993 73.12488167783042 chr2 243199373 570402707 2.3454119143637757 47.87702069394153 chr3 198022430 451465832 2.2798721942761735 4.930517778215499 chr4 191154276 395931612 2.0712673568442694 13.662955623998334 chr5 180915260 318918994 1.7628086983928277 3.090553408377517 chr6 171115067 326469256 1.907893102131094 8.87337523921247 chr7 159138663 371540485 2.3346965344304795 18.908613222884398 chr8 146364022 340775402 2.328273009606145 23.60132269152055 chr9 141213431 314017948 2.2237116241443067 22.660805295313793 chr10 135534747 319742663 2.3591194883773974 50.0511446601646 chr11 135006516 298158041 2.2084714859244277 14.689200987916603 chr12 133851895 246459016 1.8412814850323935 3.40331801898903 chr13 115169878 203993512 1.771240150137174 2.102609066927333 chr14 107349540 145146018 1.352087936287384 12.715821957325916 chr15 102531392 171874705 1.6763129969014758 2.370844654123569 chr16 90354753 234144899 2.591395485304464 24.538134136201105 chr17 81195210 133347231 1.6423041580901139 7.339522761804697 chr18 78077248 253969451 3.252797165699283 27.65174314765097 chr19 59128983 135459821 2.290920867013728 33.818240416981034 chr20 63025520 124774465 1.9797451096000478 6.10910575151191 chr21 48129895 92540705 1.92272817133717 8.871186368893273 chr22 51304566 71165997 1.3871279410101627 2.21742814285101 chrMT 16571 1420126 85.69947498642206 18.894994720776424 chrX 155270560 425912466 2.743034262258087 9.764460821966164 chrY 59373566 20895519 0.3519330302646804 16.36644174001834