BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038443.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 17,629,564 number of mapped reads = 16,619,629 (94.27%) number of supplementary alignments = 250,314 (1.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,437,394 number of mapped paired reads (second in pair) = 8,182,235 number of mapped paired reads (both in pair) = 16,317,002 number of mapped paired reads (singletons) = 302,627 number of mapped bases = 2,254,781,010 bp number of sequenced bases = 2,253,254,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,233,159 duplication rate = 13.38% >>>>>>> Insert size mean insert size = 85,997.4973 std insert size = 2,861,066.4773 median insert size = 259 >>>>>>> Mapping quality mean mapping quality = 53.4355 >>>>>>> ACTG content number of A's = 650,943,360 bp (28.89%) number of C's = 442,299,426 bp (19.63%) number of T's = 664,795,799 bp (29.5%) number of G's = 495,039,129 bp (21.97%) number of N's = 177,246 bp (0.01%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 29,744,830 number of insertions = 385,224 mapped reads with insertion percentage = 2.21% number of deletions = 793,602 mapped reads with deletion percentage = 4.61% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 0.7284X std coverageData = 10.795X There is a 28.1% of reference with a coverageData >= 1X There is a 16.02% of reference with a coverageData >= 2X There is a 9.06% of reference with a coverageData >= 3X There is a 5.52% of reference with a coverageData >= 4X There is a 3.36% of reference with a coverageData >= 5X There is a 2.11% of reference with a coverageData >= 6X There is a 1.35% of reference with a coverageData >= 7X There is a 0.88% of reference with a coverageData >= 8X There is a 0.58% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 200640641 0.8049754909136214 15.747298488674073 chr2 243199373 205028399 0.8430465772623518 11.023675114986455 chr3 198022430 159817419 0.8070672549569259 1.8090729440012108 chr4 191154276 98945953 0.5176235398469454 8.699012799485866 chr5 180915260 139094430 0.7688374656731555 1.6459189532342962 chr6 171115067 136336857 0.7967554195563621 9.628795915230207 chr7 159138663 110956227 0.6972298554500235 11.77751136205494 chr8 146364022 148799079 1.0166369915688707 4.119471429294745 chr9 141213431 97613985 0.6912514221115412 17.661719090780288 chr10 135534747 123983576 0.9147733606644797 28.65671870409328 chr11 135006516 103618277 0.7675057476485061 9.27448819300987 chr12 133851895 93906333 0.7015689467825614 1.699352170834839 chr13 115169878 79171723 0.6874342872882092 1.5074874157233962 chr14 107349540 74227138 0.6914527812601712 1.638101270132417 chr15 102531392 60637967 0.5914087950741954 1.4234857829619996 chr16 90354753 71468022 0.7909713615176392 10.933805297611046 chr17 81195210 53245929 0.6557767262379147 12.08542841464673 chr18 78077248 91513532 1.172089620781716 12.169829193886535 chr19 59128983 27296928 0.46165055806895916 6.392629830743377 chr20 63025520 57438344 0.9113505767187641 3.0951540715130625 chr21 48129895 22026872 0.45765468634411105 3.92843315928129 chr22 51304566 11794637 0.22989448931309545 0.8496236939698302 chrMT 16571 5520955 333.1696940438115 171.8871307895364 chrX 155270560 77337179 0.4980801189871409 2.4041518797741492 chrY 59373566 4360608 0.07344359272609632 8.10520760324657