BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975316.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,658,720 number of mapped reads = 2,622,815 (98.65%) number of supplementary alignments = 30,377 (1.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,313,496 number of mapped paired reads (second in pair) = 1,309,319 number of mapped paired reads (both in pair) = 2,613,574 number of mapped paired reads (singletons) = 9,241 number of mapped bases = 351,980,005 bp number of sequenced bases = 351,725,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 418,963 duplication rate = 15.75% >>>>>>> Insert size mean insert size = 86,903.7505 std insert size = 2,838,056.0119 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 53.6562 >>>>>>> ACTG content number of A's = 102,710,324 bp (29.2%) number of C's = 71,622,603 bp (20.36%) number of T's = 102,723,187 bp (29.21%) number of G's = 74,647,498 bp (21.22%) number of N's = 21,672 bp (0.01%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 3,619,111 number of insertions = 66,232 mapped reads with insertion percentage = 2.4% number of deletions = 135,660 mapped reads with deletion percentage = 4.98% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.1137X std coverageData = 1.2578X There is a 6.28% of reference with a coverageData >= 1X There is a 3.6% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 32673652 0.13108754501357892 1.34875164145757 chr2 243199373 30799071 0.12664124343774522 1.3200855489277465 chr3 198022430 22784139 0.11505837495277682 0.4982778695711066 chr4 191154276 22916280 0.11988369017703794 1.0239090678882012 chr5 180915260 21720344 0.12005810897322867 0.49286359733117535 chr6 171115067 26441311 0.15452356980347032 1.0353955770686052 chr7 159138663 20420351 0.12831797512336773 1.3471380123230203 chr8 146364022 17672714 0.120744932795028 0.6059547585455154 chr9 141213431 15407629 0.10910880707940593 2.10862022858689 chr10 135534747 17945925 0.13240829674474547 3.2243421423510505 chr11 135006516 13228531 0.09798438913866943 1.2545988766003435 chr12 133851895 15497201 0.11577871945705363 0.48147117618910173 chr13 115169878 11729175 0.10184238451654867 0.4531553099837346 chr14 107349540 10531085 0.09810088613328012 0.4569885929688651 chr15 102531392 10299061 0.10044788039159754 0.44905678409952066 chr16 90354753 11940293 0.13214903038913736 1.6887213142190434 chr17 81195210 7857029 0.09676714919513109 1.0510686349669074 chr18 78077248 9266702 0.1186863297230968 1.942566402486491 chr19 59128983 4942460 0.08358777285244362 0.8494994046064351 chr20 63025520 7530534 0.11948388525790822 0.5797283962596829 chr21 48129895 4551498 0.09456696300708738 0.6513949507586009 chr22 51304566 3836725 0.07478330486218322 0.39259465133078936 chrMT 16571 71993 4.344517530625792 3.411088149461276 chrX 155270560 10939308 0.0704532011734871 0.5275747130640605 chrY 59373566 976994 0.016455033204507204 1.1163449963043386