BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124943.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 = 4,430,976 number of mapped reads = 4,393,273 (99.15%) number of supplementary alignments = 22,651 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,198,912 number of mapped paired reads (second in pair) = 2,194,361 number of mapped paired reads (both in pair) = 4,377,216 number of mapped paired reads (singletons) = 16,057 number of mapped bases = 393,767,820 bp number of sequenced bases = 393,573,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 257,429 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 47,583.8535 std insert size = 2,048,553.7397 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.1595 >>>>>>> ACTG content number of A's = 112,493,040 bp (28.58%) number of C's = 74,883,365 bp (19.03%) number of T's = 117,440,998 bp (29.84%) number of G's = 88,749,772 bp (22.55%) number of N's = 6,089 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 2,868,916 number of insertions = 47,061 mapped reads with insertion percentage = 1.05% number of deletions = 119,098 mapped reads with deletion percentage = 2.66% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.1272X std coverageData = 1.315X There is a 9.11% of reference with a coverageData >= 1X There is a 2.22% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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% 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 32252603 0.12939828543095183 1.2707576173225565 chr2 243199373 27384268 0.1126000764812827 1.1775324595118133 chr3 198022430 33166420 0.16748819818037786 0.534362800265837 chr4 191154276 19840637 0.10379384346076569 0.9424264129928918 chr5 180915260 18585605 0.10273099682138477 0.4115942914267541 chr6 171115067 28750322 0.16801747796995573 1.5384044802585097 chr7 159138663 20338331 0.1278025755438199 1.5540266458385277 chr8 146364022 28011382 0.19138160879454377 0.7567663684824188 chr9 141213431 16757556 0.11866828729626999 1.5552882282359977 chr10 135534747 21229024 0.15663159794735146 3.7953311926532654 chr11 135006516 19341274 0.14326178152764124 1.482604994364197 chr12 133851895 18036766 0.13475166713179518 0.475825161458591 chr13 115169878 14063345 0.12210957625569421 0.43353439456429466 chr14 107349540 11867478 0.11054987287323262 0.46071949652613137 chr15 102531392 8681972 0.08467623262151752 0.3731446831592409 chr16 90354753 8101773 0.08966626249313082 1.1904096698952638 chr17 81195210 9005153 0.11090744146114039 1.5199491832568066 chr18 78077248 13172274 0.16870822598665364 1.8878744559063059 chr19 59128983 6107568 0.10329228899472193 0.8160575095941994 chr20 63025520 10430472 0.16549600860096036 0.5814889446521463 chr21 48129895 4695356 0.09755591613071252 0.5194645134470295 chr22 51304566 3247882 0.06330590536522616 0.3324835580905272 chrMT 16571 45546 2.748536600084485 2.3443666675677033 chrX 155270560 19709131 0.12693411423260148 0.7204126298591889 chrY 59373566 945682 0.015927660467622916 0.8830511745138747