BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006195.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 3,526,788 number of mapped reads = 1,606,389 (45.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 804,488 number of mapped paired reads (second in pair) = 801,901 number of mapped paired reads (both in pair) = 1,452,580 number of mapped paired reads (singletons) = 153,809 number of mapped bases = 62,088,927 bp number of sequenced bases = 62,080,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,740 duplication rate = 2.35% >>>>>>> Insert size mean insert size = 46,510.5535 std insert size = 2,062,954.278 median insert size = 95 >>>>>>> Mapping quality mean mapping quality = 47.3563 >>>>>>> ACTG content number of A's = 17,040,858 bp (27.45%) number of C's = 13,612,392 bp (21.93%) number of T's = 17,370,045 bp (27.98%) number of G's = 14,053,981 bp (22.64%) number of N's = 3,022 bp (0%) GC percentage = 44.57% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 184,773 number of insertions = 2,090 mapped reads with insertion percentage = 0.13% number of deletions = 6,517 mapped reads with deletion percentage = 0.41% homopolymer indels = 41.21% >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.2137X There is a 1.73% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% 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 5323907 0.0213596539043327 0.20784737469190626 chr2 243199373 5321525 0.021881326972006628 0.34195634396732727 chr3 198022430 4040479 0.020404148156347744 0.15989198403231392 chr4 191154276 3955047 0.020690340194116297 0.1699677275844631 chr5 180915260 3716994 0.020545497378164784 0.37232161195252766 chr6 171115067 3570204 0.020864346212131044 0.1987212709441922 chr7 159138663 3291373 0.020682422096257022 0.18609876108836537 chr8 146364022 2966536 0.02026820498277917 0.19617835384040044 chr9 141213431 2507262 0.017755124156709993 0.15802994924029418 chr10 135534747 3015600 0.02224964495635942 0.1904679951663839 chr11 135006516 2842189 0.021052235730607254 0.17533054512358967 chr12 133851895 2720708 0.020326256867711882 0.16108704772010454 chr13 115169878 1919398 0.01666579867350385 0.1445014597627377 chr14 107349540 1890350 0.017609297627171946 0.2632273350355568 chr15 102531392 1883609 0.018371046791211026 0.1521476865305312 chr16 90354753 1903729 0.02106949481672536 0.1725019717564985 chr17 81195210 1810498 0.0222980887665664 0.1761167127052607 chr18 78077248 1639268 0.020995463364692362 0.20056116673640528 chr19 59128983 1247790 0.02110284900384639 0.18852274608806055 chr20 63025520 1459474 0.023156873596600236 0.1742849644135138 chr21 48129895 837718 0.01740535689928266 0.20051289630620966 chr22 51304566 781117 0.015225097119036149 0.1581316174926157 chrMT 16571 1248 0.07531229255929033 0.31859573781613554 chrX 155270560 3280669 0.021128725239349944 0.16763626514290955 chrY 59373566 162235 0.0027324449402281142 0.08138892422398754