BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006445.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 = 1,327,971 number of mapped reads = 1,271,932 (95.78%) number of supplementary alignments = 3,211 (0.24%) number of secondary alignments = 0 number of mapped bases = 71,906,498 bp number of sequenced bases = 71,883,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,794 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8885 >>>>>>> ACTG content number of A's = 20,414,413 bp (28.4%) number of C's = 15,118,473 bp (21.03%) number of T's = 20,534,500 bp (28.57%) number of G's = 15,814,541 bp (22%) number of N's = 2,069 bp (0%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 300,997 number of insertions = 4,422 mapped reads with insertion percentage = 0.35% number of deletions = 13,692 mapped reads with deletion percentage = 1.07% homopolymer indels = 46.78% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.1956X There is a 2.13% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 5888207 0.023623640239596434 0.23776396133114136 chr2 243199373 6070939 0.024962806955920895 0.1931376274603474 chr3 198022430 4838860 0.02443591869870499 0.16610272851008173 chr4 191154276 4653643 0.024344958937774427 0.17034836518171273 chr5 180915260 4403160 0.02433824543048497 0.1662389254014189 chr6 171115067 4243773 0.024800697416084348 0.17423704267686477 chr7 159138663 3927142 0.024677485194154233 0.19732141333791428 chr8 146364022 3680848 0.025148584670623496 0.386709974033025 chr9 141213431 3044679 0.021560831561411465 0.17383212028551892 chr10 135534747 3352119 0.024732543308617384 0.18993362280170495 chr11 135006516 3308003 0.024502543269837435 0.1785886625830465 chr12 133851895 3308452 0.024717259326063334 0.1682452953689233 chr13 115169878 2244770 0.01949094710337368 0.14863993422337446 chr14 107349540 2232791 0.020799260062036595 0.15657619667237374 chr15 102531392 2203386 0.021489867220372858 0.15669191865755502 chr16 90354753 2261460 0.02502867779407244 0.18210535395600128 chr17 81195210 2116356 0.026065035117219353 0.1782101940515983 chr18 78077248 1920961 0.024603338990636554 0.23134435345612245 chr19 59128983 1544928 0.02612810032602793 0.2120226509080166 chr20 63025520 1619723 0.02569947856043076 0.17282905533411622 chr21 48129895 1344630 0.027937521991269667 0.18968213806392825 chr22 51304566 965909 0.018826959768064307 0.15437592652479404 chrMT 16571 32247 1.9459899824995475 2.448359031849323 chrX 155270560 2135801 0.01375535066016378 0.128968380413514 chrY 59373566 563711 0.009494309302560672 0.12752873588024966