BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536752.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 23,174,906 number of mapped reads = 22,374,858 (96.55%) number of supplementary alignments = 551 (0%) number of secondary alignments = 0 number of mapped bases = 1,115,869,369 bp number of sequenced bases = 1,115,775,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,513 duplication rate = 0.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3523 >>>>>>> ACTG content number of A's = 344,239,758 bp (30.85%) number of C's = 211,656,902 bp (18.97%) number of T's = 343,980,386 bp (30.83%) number of G's = 215,518,430 bp (19.32%) number of N's = 380,408 bp (0.03%) GC percentage = 38.29% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,705,587 number of insertions = 58,876 mapped reads with insertion percentage = 0.26% number of deletions = 56,359 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.17% >>>>>>> Coverage mean coverageData = 0.3605X std coverageData = 0.6659X There is a 27.67% of reference with a coverageData >= 1X There is a 6.64% of reference with a coverageData >= 2X There is a 1.4% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.01% 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 85566630 0.34329555391559086 0.6612475907950013 chr2 243199373 103395444 0.42514683621326604 0.7094513424478067 chr3 198022430 86378698 0.4362066357836332 0.7141365904156134 chr4 191154276 92953624 0.4862754103392382 0.7522871158297929 chr5 180915260 80149747 0.44302369518193213 0.720992907146572 chr6 171115067 75851358 0.44327690909883466 0.7241196741561842 chr7 159138663 64017348 0.4022740093021895 0.6994236545961043 chr8 146364022 62397298 0.42631581960763554 0.708786106606228 chr9 141213431 46408835 0.32864320816622605 0.6433676492841762 chr10 135534747 47612910 0.3512967047483403 0.6434827876387753 chr11 135006516 49786621 0.368771985790671 0.6732992877296203 chr12 133851895 51552045 0.38514243672082493 0.686097168549947 chr13 115169878 47089114 0.4088665788115188 0.7111248777671253 chr14 107349540 35629291 0.33189980134055536 0.6469963042125715 chr15 102531392 29949751 0.292103232149623 0.6094620892801952 chr16 90354753 20078042 0.22221345677299345 0.5233292317462892 chr17 81195210 17685329 0.2178124670162193 0.5222423137042359 chr18 78077248 33810957 0.4330449377519044 0.7159419053704202 chr19 59128983 7775291 0.1314971204561391 0.3940969200192036 chr20 63025520 17011222 0.26991006182892263 0.5784156229577395 chr21 48129895 14288123 0.29686586683806393 0.6314435860705631 chr22 51304566 5618942 0.109521285103552 0.3659860127491984 chrMT 16571 979 0.05907911411502022 0.2554294315723828 chrX 155270560 35778938 0.2304296319920531 0.5053682773345913 chrY 59373566 5082832 0.08560765913908557 0.3273683064888387