BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975257.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,973,390 number of mapped reads = 5,935,498 (99.37%) number of supplementary alignments = 15,290 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,967,502 number of mapped paired reads (second in pair) = 2,967,996 number of mapped paired reads (both in pair) = 5,924,766 number of mapped paired reads (singletons) = 10,732 number of mapped bases = 549,557,031 bp number of sequenced bases = 549,320,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,009 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 60,549.3595 std insert size = 2,381,289.6749 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.8939 >>>>>>> ACTG content number of A's = 157,466,313 bp (28.67%) number of C's = 109,350,679 bp (19.91%) number of T's = 163,323,281 bp (29.73%) number of G's = 119,172,346 bp (21.69%) number of N's = 7,616 bp (0%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 3,367,697 number of insertions = 75,240 mapped reads with insertion percentage = 1.25% number of deletions = 140,078 mapped reads with deletion percentage = 2.32% homopolymer indels = 46.02% >>>>>>> Coverage mean coverageData = 0.1775X std coverageData = 1.0355X There is a 11.9% of reference with a coverageData >= 1X There is a 3.84% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 54851950 0.2200674557195988 1.064962390659047 chr2 243199373 35269509 0.14502302602564687 1.1318415101677788 chr3 198022430 29677737 0.1498705828425598 0.5133136743727906 chr4 191154276 20085757 0.10507615848467863 0.5469252613024307 chr5 180915260 31151767 0.1721898252253569 0.5333629561244464 chr6 171115067 37382835 0.21846606295633803 1.1050359455262517 chr7 159138663 36341727 0.2283651647871391 1.254781568352465 chr8 146364022 25289577 0.17278547456150117 0.6239959981831272 chr9 141213431 18766347 0.13289349934426564 1.0245682371075548 chr10 135534747 26356846 0.19446560076583166 2.544280430337652 chr11 135006516 29260884 0.2167368277246707 0.8621749273554025 chr12 133851895 28310937 0.21150942241049334 0.6030067906929235 chr13 115169878 35875191 0.3114980377073943 0.8052036415531926 chr14 107349540 16942442 0.1578250079134014 0.5332202482439895 chr15 102531392 10301070 0.10046747439067247 0.4002362533495049 chr16 90354753 22746911 0.2517511281337906 1.5920703700761751 chr17 81195210 14932814 0.18391249927181666 1.420674328711886 chr18 78077248 12369206 0.15842266879078526 1.5138716970671753 chr19 59128983 5542424 0.09373447197628954 0.6218778125521154 chr20 63025520 14975607 0.23761179598359522 0.6566403214424186 chr21 48129895 6361828 0.13218038393809087 0.5024484858981803 chr22 51304566 4221974 0.08229236360755883 0.3672182315649214 chrMT 16571 48466 2.9247480538289783 2.7700782137852746 chrX 155270560 31690058 0.2040957281277275 0.7282289566817092 chrY 59373566 803167 0.013527349864752944 0.5564295180873331