BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124974.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 = 2,521,208 number of mapped reads = 2,476,223 (98.22%) number of supplementary alignments = 55,877 (2.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,245,668 number of mapped paired reads (second in pair) = 1,230,555 number of mapped paired reads (both in pair) = 2,458,658 number of mapped paired reads (singletons) = 17,565 number of mapped bases = 312,575,733 bp number of sequenced bases = 312,311,098 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 475,799 duplication rate = 16.56% >>>>>>> Insert size mean insert size = 85,986.4025 std insert size = 2,733,017.0261 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.1852 >>>>>>> ACTG content number of A's = 90,546,674 bp (28.99%) number of C's = 61,795,683 bp (19.79%) number of T's = 92,088,033 bp (29.49%) number of G's = 67,878,286 bp (21.73%) number of N's = 2,422 bp (0%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 3,188,429 number of insertions = 67,086 mapped reads with insertion percentage = 2.52% number of deletions = 118,582 mapped reads with deletion percentage = 4.58% homopolymer indels = 45.07% >>>>>>> Coverage mean coverageData = 0.101X std coverageData = 1.7495X There is a 5.76% of reference with a coverageData >= 1X There is a 2.66% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% 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 0.01% 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% 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 26674950 0.10702059594868572 1.450640669474328 chr2 243199373 25631524 0.1053930513217236 1.6255706423208303 chr3 198022430 21712628 0.10964731621564285 0.5137671014817596 chr4 191154276 16540328 0.08652868429686605 1.7867894113730693 chr5 180915260 16841264 0.09308923968050015 0.438444097720389 chr6 171115067 17865236 0.10440480965945564 0.7868402751412752 chr7 159138663 21621897 0.13586828362382308 1.3427312270995337 chr8 146364022 21125475 0.1443351631864831 0.7022911312250666 chr9 141213431 11572785 0.08195243836260872 1.6747321883727129 chr10 135534747 17032335 0.12566766365823517 5.906845575736113 chr11 135006516 10502064 0.0777893120358724 0.6600469616124303 chr12 133851895 14385397 0.10747249413241404 0.4647469352082359 chr13 115169878 6945147 0.06030350227513482 0.3410799491060701 chr14 107349540 12672297 0.1180470545099681 0.5149320081387472 chr15 102531392 7769717 0.07577890876581486 0.39341312538121315 chr16 90354753 11912135 0.13183739210708706 2.659318507124882 chr17 81195210 6507722 0.08014908761243428 1.2374567343084761 chr18 78077248 4927913 0.06311586443210704 1.611976734838374 chr19 59128983 4784221 0.08091160641136005 0.8442730334026676 chr20 63025520 6872891 0.1090493343014068 0.7335063883325345 chr21 48129895 3287049 0.06829537026831245 1.0320625289813061 chr22 51304566 2261731 0.044084399817357386 0.3241589164403089 chrMT 16571 415413 25.068674189849737 14.86681866985248 chrX 155270560 15376646 0.09903130380929907 0.5471801304927179 chrY 59373566 7336968 0.12357297185080647 3.4694889137596503