BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080787.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,007,469 number of mapped reads = 2,546,551 (84.67%) number of supplementary alignments = 25,173 (0.84%) number of secondary alignments = 0 number of mapped bases = 163,433,052 bp number of sequenced bases = 163,378,852 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,725 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6146 >>>>>>> ACTG content number of A's = 47,364,279 bp (28.99%) number of C's = 32,694,071 bp (20.01%) number of T's = 48,290,595 bp (29.56%) number of G's = 35,026,537 bp (21.44%) number of N's = 3,370 bp (0%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,250,185 number of insertions = 11,959 mapped reads with insertion percentage = 0.47% number of deletions = 34,458 mapped reads with deletion percentage = 1.34% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.0528X std coverageData = 0.351X There is a 4.18% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% 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 20761293 0.08329484964452706 0.5645172311409881 chr2 243199373 12497869 0.05138939646855093 0.4189864384775244 chr3 198022430 9677402 0.0488702315187224 0.27029445538358104 chr4 191154276 9384321 0.04909291696932796 0.2777319664127978 chr5 180915260 12625109 0.0697846549815643 0.3233532184805294 chr6 171115067 11506700 0.06724539341705076 0.3877843577906089 chr7 159138663 10929574 0.068679564060432 0.44462300180448106 chr8 146364022 7601974 0.05193881594754208 0.40150247691823715 chr9 141213431 5323138 0.037695691991224266 0.2767410258092539 chr10 135534747 6728773 0.04964611030704916 0.3220614874571644 chr11 135006516 6718555 0.04976467209923408 0.30182561357704746 chr12 133851895 6561454 0.04902025481223109 0.27252654037255414 chr13 115169878 7138925 0.061986042913061 0.3083621738029357 chr14 107349540 4232634 0.03942852479852266 0.2531295651494478 chr15 102531392 4135475 0.040333744810564946 0.26127434594925375 chr16 90354753 3818671 0.04226308935845356 0.2646032915246686 chr17 81195210 4500274 0.05542536314642206 0.30755292429742476 chr18 78077248 1998181 0.025592359505294038 0.3682619089235331 chr19 59128983 2523730 0.042681775872925126 0.3921300611535102 chr20 63025520 2925058 0.04641069204982363 0.2658929815046859 chr21 48129895 2582942 0.05366606347260886 0.28949906199293474 chr22 51304566 846986 0.016508978947409866 0.15611461038974808 chrMT 16571 52095 3.143745096855953 2.5991569185046375 chrX 155270560 8021838 0.05166361221341637 0.29155191253300233 chrY 59373566 340081 0.005727818335856735 0.10845787860845792