BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472491.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,261,606 number of mapped reads = 15,040,497 (98.55%) number of supplementary alignments = 71,009 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,528,188 number of mapped paired reads (second in pair) = 7,512,309 number of mapped paired reads (both in pair) = 14,916,314 number of mapped paired reads (singletons) = 124,183 number of mapped bases = 1,475,846,027 bp number of sequenced bases = 1,475,674,761 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,144,328 duplication rate = 44.72% >>>>>>> Insert size mean insert size = 38,921.2634 std insert size = 1,942,516.7451 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 54.9795 >>>>>>> ACTG content number of A's = 415,683,330 bp (28.17%) number of C's = 329,098,507 bp (22.3%) number of T's = 405,434,999 bp (27.47%) number of G's = 325,233,713 bp (22.04%) number of N's = 224,212 bp (0.02%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 12,573,275 number of insertions = 77,066 mapped reads with insertion percentage = 0.51% number of deletions = 71,556 mapped reads with deletion percentage = 0.47% homopolymer indels = 44.75% >>>>>>> Coverage mean coverageData = 0.4767X std coverageData = 16.0871X There is a 4.81% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 165680363 0.6647139426786022 19.90966284857057 chr2 243199373 100173721 0.4118995857773038 13.41617832642985 chr3 198022430 155601255 0.7857759093250194 18.031882814464193 chr4 191154276 67117583 0.35111735088782425 14.907044027035969 chr5 180915260 79795262 0.4410642971742682 16.410432749466555 chr6 171115067 97172353 0.5678772460171494 16.72714139338579 chr7 159138663 67459478 0.42390376246908645 16.093022599109695 chr8 146364022 72001439 0.4919340013763765 18.55253902979012 chr9 141213431 84445749 0.5980008303884352 14.24673828746511 chr10 135534747 36432390 0.2688047958653732 10.4870053854941 chr11 135006516 71979505 0.533155784865969 14.87659204054621 chr12 133851895 67181950 0.5019125803187172 14.410502253992066 chr13 115169878 34719729 0.30146536232329774 12.360256289903607 chr14 107349540 32061940 0.29866862960008955 9.627965373409568 chr15 102531392 39658710 0.38679578250532287 16.223712365212137 chr16 90354753 36527147 0.40426370265214495 9.998734919421953 chr17 81195210 51791089 0.6378589204954331 14.673121931553446 chr18 78077248 26628861 0.3410578841098498 13.098232453573159 chr19 59128983 34088056 0.5765033367815577 18.779515116669508 chr20 63025520 28784523 0.45671218579394507 14.127611203302363 chr21 48129895 5122218 0.10642487377128082 2.9598628522681243 chr22 51304566 11604655 0.2261914660773078 6.508775678835941 chrMT 16571 4270 0.25767907790718725 0.8491717219326382 chrX 155270560 103730915 0.6680655689011491 28.670067042262932 chrY 59373566 6082866 0.10245074382091182 8.310164970347675