BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124982.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,897,572 number of mapped reads = 5,793,969 (98.24%) number of supplementary alignments = 58,994 (1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,903,647 number of mapped paired reads (second in pair) = 2,890,322 number of mapped paired reads (both in pair) = 5,763,572 number of mapped paired reads (singletons) = 30,397 number of mapped bases = 495,543,906 bp number of sequenced bases = 495,245,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 653,684 duplication rate = 7.49% >>>>>>> Insert size mean insert size = 95,421.9639 std insert size = 2,900,358.7205 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 52.3563 >>>>>>> ACTG content number of A's = 141,856,257 bp (28.64%) number of C's = 91,147,363 bp (18.4%) number of T's = 150,042,485 bp (30.3%) number of G's = 112,194,189 bp (22.65%) number of N's = 5,248 bp (0%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 3,805,929 number of insertions = 78,593 mapped reads with insertion percentage = 1.31% number of deletions = 158,611 mapped reads with deletion percentage = 2.67% homopolymer indels = 45.69% >>>>>>> Coverage mean coverageData = 0.1601X std coverageData = 2.1137X There is a 10.66% of reference with a coverageData >= 1X There is a 3.01% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 40450303 0.16228767189310234 1.6118141747318984 chr2 243199373 46489588 0.19115833822482758 2.5363460875127677 chr3 198022430 33433452 0.16883669188384368 0.6196731364163035 chr4 191154276 32825167 0.171720809426204 1.6675277862995883 chr5 180915260 29258815 0.16172662825678719 0.5751319235564659 chr6 171115067 28100406 0.16421935538850008 0.8939926337392348 chr7 159138663 27721995 0.17420025075867326 1.4469396419577156 chr8 146364022 26385579 0.18027366725410157 0.7920916956682624 chr9 141213431 20573725 0.14569240938561998 2.099995947495444 chr10 135534747 27996333 0.20656203386722669 7.206239186982747 chr11 135006516 21210581 0.15710783174346932 1.0612766386803019 chr12 133851895 23465115 0.1753065580431267 0.5686025130699146 chr13 115169878 14272243 0.12392340122128113 0.4631044531336201 chr14 107349540 14951031 0.13927429032299532 0.6313192603895317 chr15 102531392 13339934 0.13010585089881546 0.49692659220663693 chr16 90354753 16558493 0.18326089608147123 3.302324686345747 chr17 81195210 11012475 0.13562961411147284 1.6001759049495763 chr18 78077248 13187697 0.1689057611251872 2.253315920517306 chr19 59128983 6992001 0.11824997903312492 0.9699176649101742 chr20 63025520 10416978 0.16528190485377986 0.7332942447332015 chr21 48129895 5932611 0.12326249620947646 0.8523486065477589 chr22 51304566 4558965 0.08886080431905417 0.4744677400038355 chrMT 16571 352373 21.264437873393277 12.420233309890287 chrX 155270560 18206408 0.11725602071635473 0.7102315353535672 chrY 59373566 7851638 0.1322413075205892 3.2418150378330584