BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124881.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 = 5,178,716 number of mapped reads = 5,084,670 (98.18%) number of supplementary alignments = 23,158 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,543,864 number of mapped paired reads (second in pair) = 2,540,806 number of mapped paired reads (both in pair) = 5,066,276 number of mapped paired reads (singletons) = 18,394 number of mapped bases = 465,076,036 bp number of sequenced bases = 464,813,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 278,233 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 73,380.3858 std insert size = 2,589,056.5522 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 52.693 >>>>>>> ACTG content number of A's = 132,058,068 bp (28.41%) number of C's = 94,141,557 bp (20.25%) number of T's = 136,134,053 bp (29.29%) number of G's = 102,472,169 bp (22.05%) number of N's = 7,974 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 3,526,131 number of insertions = 65,774 mapped reads with insertion percentage = 1.26% number of deletions = 153,502 mapped reads with deletion percentage = 2.96% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.1502X std coverageData = 1.5045X There is a 9.72% of reference with a coverageData >= 1X There is a 3.12% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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% 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 38784866 0.15560589516043774 1.5964644210381373 chr2 243199373 34581423 0.14219371774449435 1.7650595135033407 chr3 198022430 44555841 0.22500401090926922 0.7168431738572809 chr4 191154276 27199781 0.14229229692983691 0.9030930495163565 chr5 180915260 27023001 0.14936827882844156 0.5172414409152954 chr6 171115067 26441532 0.15452486133205323 1.7937959905261225 chr7 159138663 26031911 0.16358005345313226 2.0611888856477645 chr8 146364022 31421098 0.21467774368758463 0.7705481386098803 chr9 141213431 19694879 0.13946887955721435 2.0978100572676954 chr10 135534747 22103403 0.16308292514833853 3.256834410021535 chr11 135006516 22768662 0.16864861544904988 1.3963144270038519 chr12 133851895 18486518 0.1381117390979037 0.4915328477101373 chr13 115169878 11897641 0.10330514546520575 0.43314231579492757 chr14 107349540 16089505 0.14987958960979245 0.5813592154500116 chr15 102531392 8668846 0.08454821329256897 0.378568537401592 chr16 90354753 13632987 0.1508828982134454 2.4924457198957413 chr17 81195210 9805601 0.12076575699477839 1.3281097334061358 chr18 78077248 15221280 0.19495154337406975 2.343187329660634 chr19 59128983 10392960 0.17576760960018542 1.08910465923692 chr20 63025520 11222147 0.17805719016677687 0.6070442147901688 chr21 48129895 5687471 0.11816919608904196 0.5645752256724983 chr22 51304566 4472404 0.087173605561735 0.4171534285957326 chrMT 16571 112849 6.8100295697302515 4.096450139633777 chrX 155270560 13077814 0.0842259730370007 0.703406885948516 chrY 59373566 5701616 0.09602953610702783 1.9885715766381626