BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777295.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,794,730 number of mapped reads = 1,769,925 (98.62%) number of supplementary alignments = 52,530 (2.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 887,093 number of mapped paired reads (second in pair) = 882,832 number of mapped paired reads (both in pair) = 1,761,022 number of mapped paired reads (singletons) = 8,903 number of mapped bases = 173,701,136 bp number of sequenced bases = 173,638,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,566 duplication rate = 4.96% >>>>>>> Insert size mean insert size = 159,072.4579 std insert size = 3,813,913.9329 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 53.3138 >>>>>>> ACTG content number of A's = 50,600,473 bp (29.14%) number of C's = 36,322,343 bp (20.92%) number of T's = 49,648,307 bp (28.59%) number of G's = 37,064,850 bp (21.35%) number of N's = 2,951 bp (0%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,096,751 number of insertions = 35,524 mapped reads with insertion percentage = 1.95% number of deletions = 24,049 mapped reads with deletion percentage = 1.31% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.0561X std coverageData = 0.7536X There is a 4.14% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% 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 13583164 0.05449600865788816 1.2359163719529944 chr2 243199373 15193490 0.06247339297211099 0.5031247551365626 chr3 198022430 11439478 0.05776859722406194 0.3525487349760295 chr4 191154276 11277579 0.05899726250434492 0.6742848379848861 chr5 180915260 10421177 0.05760253170462237 0.29536980384803013 chr6 171115067 9768719 0.057088596412144116 0.40134111168511083 chr7 159138663 9292147 0.05839025429037317 0.481268067825815 chr8 146364022 8690346 0.059374878342711844 0.35775726820722026 chr9 141213431 7318548 0.05182614676361769 0.62202815260723 chr10 135534747 9939967 0.07333888334922704 2.2279925783126666 chr11 135006516 8240816 0.06104013527761875 0.37325401960190807 chr12 133851895 7438134 0.05556988192061084 0.2884645391896483 chr13 115169878 5260001 0.04567167293517494 0.2614235723733091 chr14 107349540 5317769 0.04953695190496391 0.2744054391774007 chr15 102531392 5023635 0.048996067467805375 0.2687702508759199 chr16 90354753 5667188 0.06272152611606387 0.4944920938437076 chr17 81195210 4970701 0.06121914088281809 0.4321203741075961 chr18 78077248 4786911 0.06130993500180744 0.7525398205390217 chr19 59128983 3404581 0.05757888648279305 0.6820635850289313 chr20 63025520 3916932 0.062148348795852855 0.33522815463508737 chr21 48129895 2392939 0.04971835072567684 0.35775062592300044 chr22 51304566 2199251 0.042866574487736626 0.2553594046428813 chrMT 16571 1626514 98.1542453684147 23.402036675235422 chrX 155270560 4775958 0.030758941038146574 0.23263379426946731 chrY 59373566 1755191 0.029561825543710816 0.6046482264919562