BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124886.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 = 5,208,350 number of mapped reads = 5,053,546 (97.03%) number of supplementary alignments = 5,680 (0.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,540,013 number of mapped paired reads (second in pair) = 2,513,533 number of mapped paired reads (both in pair) = 4,979,772 number of mapped paired reads (singletons) = 73,774 number of mapped bases = 337,186,598 bp number of sequenced bases = 337,047,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 240,136 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 36,887.7441 std insert size = 1,760,010.1844 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 51.8564 >>>>>>> ACTG content number of A's = 95,823,449 bp (28.43%) number of C's = 63,099,533 bp (18.72%) number of T's = 99,958,256 bp (29.66%) number of G's = 78,163,481 bp (23.19%) number of N's = 2,899 bp (0%) GC percentage = 41.91% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 2,300,648 number of insertions = 36,389 mapped reads with insertion percentage = 0.71% number of deletions = 93,989 mapped reads with deletion percentage = 1.84% homopolymer indels = 49.54% >>>>>>> Coverage mean coverageData = 0.1089X std coverageData = 0.9634X There is a 8.32% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% 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 0.02% 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% 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 23698376 0.09507850333500273 1.3609298386308375 chr2 243199373 29748928 0.12232321010136815 1.052528069140747 chr3 198022430 19916739 0.10057819712645684 0.37787762903139827 chr4 191154276 14575051 0.07624758025292618 0.4552966198833074 chr5 180915260 15523051 0.08580288362629002 0.34104628044880453 chr6 171115067 22805015 0.13327298057277445 0.9403364963255971 chr7 159138663 20517997 0.1289315658005748 1.3476283872288888 chr8 146364022 25883785 0.1768452700760027 0.6357398339746395 chr9 141213431 12320019 0.08724396052667256 0.8615206172454147 chr10 135534747 16605482 0.1225182646336441 2.175769854445469 chr11 135006516 22155052 0.16410357556371574 0.8225271781554799 chr12 133851895 10834782 0.08094604861589745 0.33603472323997635 chr13 115169878 19250050 0.16714483278344708 0.728884414854255 chr14 107349540 5214243 0.04857256957039592 0.3062899675498581 chr15 102531392 7029693 0.06856137289153355 0.31150237044678014 chr16 90354753 10176871 0.11263238138673236 1.6936300621255775 chr17 81195210 4441356 0.05469972920816388 0.769249858655158 chr18 78077248 9190552 0.11771101358490504 1.3589859153302872 chr19 59128983 5212864 0.08816089395618389 0.8699777048612113 chr20 63025520 8555705 0.13574985180606206 0.45485646175732514 chr21 48129895 2715427 0.05641871855319859 0.33162217857698495 chr22 51304566 2399083 0.04676158843249936 0.24735922825473936 chrMT 16571 268645 16.211755476434735 10.003663797615566 chrX 155270560 27480517 0.1769847226673234 0.7015334021414767 chrY 59373566 667315 0.01123926091958162 0.4983385150245899