BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472453.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 = 13,406,166 number of mapped reads = 13,271,829 (99%) number of supplementary alignments = 48,029 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,655,963 number of mapped paired reads (second in pair) = 6,615,866 number of mapped paired reads (both in pair) = 13,213,268 number of mapped paired reads (singletons) = 58,561 number of mapped bases = 1,294,326,510 bp number of sequenced bases = 1,294,169,705 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,473,387 duplication rate = 46.61% >>>>>>> Insert size mean insert size = 18,470.8828 std insert size = 1,404,029.4256 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 54.4633 >>>>>>> ACTG content number of A's = 342,826,247 bp (26.49%) number of C's = 305,478,143 bp (23.6%) number of T's = 344,628,120 bp (26.63%) number of G's = 301,063,739 bp (23.26%) number of N's = 173,456 bp (0.01%) GC percentage = 46.87% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 5,785,581 number of insertions = 72,828 mapped reads with insertion percentage = 0.54% number of deletions = 59,371 mapped reads with deletion percentage = 0.44% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.4181X std coverageData = 16.27X There is a 3.53% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 200006966 0.8024331702668055 25.759884975857723 chr2 243199373 89878391 0.3695667052562672 12.977240260602045 chr3 198022430 127550485 0.6441214007928294 16.624587502638963 chr4 191154276 74148704 0.38789979252151285 15.584548393560176 chr5 180915260 50876670 0.281218234437493 12.384428458294689 chr6 171115067 115973201 0.6777497916066035 25.061991816582818 chr7 159138663 36346020 0.22839214126110888 9.7380682794194 chr8 146364022 13347623 0.09119469947334462 3.2046587470368486 chr9 141213431 48024087 0.34008158189995397 11.211802836762436 chr10 135534747 42508030 0.3136319721761092 10.987962835099172 chr11 135006516 56161967 0.4159944917029042 14.385914473263064 chr12 133851895 80483433 0.6012872137521849 17.89719111217278 chr13 115169878 30057443 0.2609835446730264 10.145733839064684 chr14 107349540 36012772 0.33547206629856074 12.037900367797215 chr15 102531392 39774277 0.3879229202311035 13.93770911002471 chr16 90354753 82121170 0.9088749321244893 37.45760414206004 chr17 81195210 78238691 0.9635875195100795 24.228000017013553 chr18 78077248 7676042 0.09831342928480266 3.1265924540237373 chr19 59128983 29174456 0.49340364944210185 11.328233392641616 chr20 63025520 27159478 0.43092826524874367 11.188784911054352 chr21 48129895 12437521 0.25841571023581084 15.888015800170425 chr22 51304566 13327733 0.2597767418985671 9.686598825761878 chrMT 16571 6303 0.38036328525737734 0.8310829224760335 chrX 155270560 2663138 0.017151596542190613 0.39858365594903716 chrY 59373566 371909 0.006263881808951815 0.7589236485665449