BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975318.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 = 5,309,872 number of mapped reads = 5,265,383 (99.16%) number of supplementary alignments = 89,524 (1.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,632,396 number of mapped paired reads (second in pair) = 2,632,987 number of mapped paired reads (both in pair) = 5,252,402 number of mapped paired reads (singletons) = 12,981 number of mapped bases = 511,746,965 bp number of sequenced bases = 511,586,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 196,398 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 190,999.2474 std insert size = 4,128,444.8786 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.4545 >>>>>>> ACTG content number of A's = 149,271,211 bp (29.18%) number of C's = 105,197,690 bp (20.56%) number of T's = 151,836,266 bp (29.68%) number of G's = 105,267,188 bp (20.58%) number of N's = 13,708 bp (0%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 2,515,331 number of insertions = 71,585 mapped reads with insertion percentage = 1.33% number of deletions = 69,055 mapped reads with deletion percentage = 1.28% homopolymer indels = 38.49% >>>>>>> Coverage mean coverageData = 0.1653X std coverageData = 1.8717X There is a 12.55% of reference with a coverageData >= 1X There is a 2.89% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 42582698 0.17084289631519112 4.861161765968788 chr2 243199373 44599759 0.18338763973704816 1.1078353511265204 chr3 198022430 34181520 0.1726143851481875 0.5380760770252645 chr4 191154276 34211275 0.17897206233566024 1.365623345856877 chr5 180915260 31182172 0.17235788733355054 0.4818146906851637 chr6 171115067 30015628 0.17541195247289357 0.7403892505772145 chr7 159138663 28171855 0.17702709366107972 1.395025789330125 chr8 146364022 25932116 0.17717548100721092 1.44483524336937 chr9 141213431 22248930 0.1575553390526996 1.6610001213869443 chr10 135534747 27688836 0.20429326510640108 3.5522485022473225 chr11 135006516 23202093 0.17185906049156915 1.0489030404406399 chr12 133851895 22786771 0.1702386880663886 0.4847677274431621 chr13 115169878 17055932 0.14809368817773688 0.4445258610361657 chr14 107349540 15575216 0.14508880056682125 0.4559264474883713 chr15 102531392 15522319 0.15139089304473696 0.45165158818211615 chr16 90354753 15433547 0.17081057152577242 1.0472038420016707 chr17 81195210 13940336 0.1716891427462285 0.7077392741371702 chr18 78077248 14449223 0.1850631697469665 1.6976690777635204 chr19 59128983 9372379 0.15850736008769167 2.355450658324924 chr20 63025520 10807864 0.17148393222301062 0.5622291632192156 chr21 48129895 7313860 0.15196085509847881 1.1834210049075191 chr22 51304566 6371917 0.12419785404675288 1.3674700004895377 chrMT 16571 456234 27.532074105364792 9.196259032299768 chrX 155270560 12913194 0.08316575917546765 0.5483010223016157 chrY 59373566 5731291 0.0965293376517085 1.8695953542956147