BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094035.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 349,008 number of mapped reads = 314,917 (90.23%) number of supplementary alignments = 18,232 (5.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 158,599 number of mapped paired reads (second in pair) = 156,318 number of mapped paired reads (both in pair) = 309,040 number of mapped paired reads (singletons) = 5,877 number of mapped bases = 39,768,419 bp number of sequenced bases = 38,994,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 287,616 duplication rate = 43.78% >>>>>>> Insert size mean insert size = 579,756.4818 std insert size = 7,107,502.4152 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 44.0189 >>>>>>> ACTG content number of A's = 11,009,820 bp (28.23%) number of C's = 8,643,946 bp (22.17%) number of T's = 10,400,222 bp (26.67%) number of G's = 8,940,346 bp (22.93%) number of N's = 396 bp (0%) GC percentage = 45.09% >>>>>>> Mismatches and indels general error rate = 0.0371 number of mismatches = 1,386,546 number of insertions = 26,052 mapped reads with insertion percentage = 8.06% number of deletions = 102,866 mapped reads with deletion percentage = 31.36% homopolymer indels = 29.16% >>>>>>> Coverage mean coverageData = 0.0128X std coverageData = 3.8533X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% 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% 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 835644 0.00335262554872431 0.9764160461712993 chr2 243199373 2024318 0.008323697446374585 2.363774504026097 chr3 198022430 717965 0.0036256751318524878 1.4117078494772555 chr4 191154276 919973 0.004812725193759202 1.36044758021426 chr5 180915260 444513 0.002457023249448388 0.650408253346642 chr6 171115067 1002402 0.005858058075037893 2.0540647381952293 chr7 159138663 1042787 0.006552694237477665 1.6374409212352723 chr8 146364022 721349 0.004928458443154835 1.7782211665283865 chr9 141213431 503343 0.00356441307626043 0.8422154454265116 chr10 135534747 692089 0.005106358445484094 1.4222053207419223 chr11 135006516 1584690 0.011737877896204655 3.224985000149705 chr12 133851895 1257435 0.009394226357422882 2.3757062811368646 chr13 115169878 485375 0.004214426622905687 0.9811486460694252 chr14 107349540 506801 0.0047210356001525485 0.7902257961970969 chr15 102531392 308029 0.0030042408865374615 0.9130959932737146 chr16 90354753 261795 0.0028974126020797158 0.7294990768883619 chr17 81195210 796137 0.009805221268594538 1.908738136898242 chr18 78077248 155094 0.0019864173491360763 0.45279292168720175 chr19 59128983 226872 0.00383690008671382 0.6794153921820429 chr20 63025520 290953 0.004616431566133845 1.2942625815835993 chr21 48129895 259711 0.005396043353096864 0.946154036331121 chr22 51304566 173579 0.0033833051038771093 0.5634788659775668 chrMT 16571 5015133 302.6451632369803 1276.0076813292985 chrX 155270560 18826553 0.12124998454310978 7.902970119835501 chrY 59373566 715879 0.012057200674118175 2.5472749742535012