BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549006.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,339,405 number of mapped reads = 9,819,262 (86.59%) number of secondary alignments = 0 number of mapped bases = 389,683,354 bp number of sequenced bases = 389,639,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 910,942 duplication rate = 8.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0969 >>>>>>> ACTG content number of A's = 116,894,288 bp (30%) number of C's = 77,018,638 bp (19.77%) number of T's = 117,469,054 bp (30.15%) number of G's = 78,253,766 bp (20.08%) number of N's = 3,955 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,142,499 number of insertions = 12,250 mapped reads with insertion percentage = 0.12% number of deletions = 33,355 mapped reads with deletion percentage = 0.34% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 0.1259X std coverageData = 0.9232X There is a 9.06% of reference with a coverageData >= 1X There is a 2.37% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% 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% 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 31408357 0.1260111484336081 1.3601773683744594 chr2 243199373 33234684 0.13665612534288893 0.687219118459199 chr3 198022430 27209739 0.1374073583482437 0.48207405197570585 chr4 191154276 27009918 0.14129905208084384 0.5419062559363222 chr5 180915260 25722197 0.14217815014609603 0.4949181158797965 chr6 171115067 23402812 0.1367665186374266 0.5640397678239603 chr7 159138663 21674168 0.1361967456016644 0.9921047684566454 chr8 146364022 20338494 0.13895828853350314 2.717782675277162 chr9 141213431 16634098 0.11779402201480396 0.6312143886562821 chr10 135534747 18859285 0.13914723284944783 0.7345344456082747 chr11 135006516 18510025 0.13710467871047055 0.6373954702981546 chr12 133851895 18357126 0.1371450587233001 0.5038387333592188 chr13 115169878 13325235 0.1157006956280704 0.4392607726824379 chr14 107349540 12233164 0.11395637093554384 0.5435281140277535 chr15 102531392 11312743 0.11033443299004465 0.4281552635259552 chr16 90354753 10376165 0.11483806502132765 0.49694153628989807 chr17 81195210 9338997 0.1150190633166661 0.48838623072880444 chr18 78077248 10637703 0.13624587536691868 1.28580607191838 chr19 59128983 6607816 0.1117525731839494 1.0702475192661451 chr20 63025520 7586814 0.12037685686686916 0.48097871646214313 chr21 48129895 5066935 0.10527625294009056 0.5274477046152136 chr22 51304566 3798164 0.07403169534657013 0.39589521939823075 chrMT 16571 22624 1.3652766881902119 1.8298575094803937 chrX 155270560 13637630 0.0878313957262729 0.49224143627523137 chrY 59373566 3378461 0.05690177005706546 0.5729591463638197