BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514743.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 3,634,186 number of mapped reads = 1,553,248 (42.74%) number of supplementary alignments = 272,020 (7.49%) number of secondary alignments = 0 number of mapped bases = 144,664,932 bp number of sequenced bases = 144,541,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 835,875 duplication rate = 28.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.647 >>>>>>> ACTG content number of A's = 45,074,469 bp (31.18%) number of C's = 26,727,292 bp (18.49%) number of T's = 44,428,861 bp (30.74%) number of G's = 28,301,613 bp (19.58%) number of N's = 9,400 bp (0.01%) GC percentage = 38.07% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 887,883 number of insertions = 91,403 mapped reads with insertion percentage = 5.64% number of deletions = 38,233 mapped reads with deletion percentage = 2.3% homopolymer indels = 49.06% >>>>>>> Coverage mean coverageData = 0.0467X std coverageData = 3.1184X There is a 0.54% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11776227 0.047246530230309836 2.1062888132080717 chr2 243199373 13841443 0.05691397485634143 3.896599744372093 chr3 198022430 16648867 0.08407566253984461 4.501644940812032 chr4 191154276 7109428 0.03719209503845993 1.883363618090493 chr5 180915260 8424401 0.04656545279817745 1.9095706459142432 chr6 171115067 6651561 0.03887186041893085 2.1191715126884594 chr7 159138663 8050385 0.05058723535964356 3.9512740010622727 chr8 146364022 9131893 0.06239165113951296 2.2932626924390918 chr9 141213431 8714004 0.061708039655236475 4.236694632956048 chr10 135534747 5204683 0.03840109724777809 1.8336859790650932 chr11 135006516 4812124 0.03564364256314858 1.9188379733331675 chr12 133851895 6316327 0.04718892474402398 1.6316933376676133 chr13 115169878 8896941 0.07725058977660808 2.6992300506825115 chr14 107349540 2677099 0.024938150643216542 1.138302533321548 chr15 102531392 2523697 0.024613895810563072 1.4568059322824558 chr16 90354753 2985089 0.03303743191019514 2.9830301388530103 chr17 81195210 1903352 0.023441678394575248 1.865674087328614 chr18 78077248 4397501 0.05632243851627557 2.536636320199435 chr19 59128983 494180 0.008357661081368506 0.4195233144440908 chr20 63025520 2292757 0.036378232182772946 2.5823205527077313 chr21 48129895 3906823 0.0811724812613865 12.450423563827652 chr22 51304566 518252 0.010101479076930502 1.3165265350336903 chrMT 16571 2620017 158.10856315249532 202.24970101397489 chrX 155270560 3521976 0.02268283182594305 1.0332906096003416 chrY 59373566 1245905 0.02098416995873214 1.0407316112074596