BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818906.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,978,575 number of mapped reads = 1,944,496 (98.28%) number of supplementary alignments = 28,216 (1.43%) number of secondary alignments = 0 number of mapped bases = 180,270,105 bp number of sequenced bases = 180,155,551 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 385,591 duplication rate = 16.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3773 >>>>>>> ACTG content number of A's = 49,809,907 bp (27.65%) number of C's = 38,092,153 bp (21.14%) number of T's = 51,614,255 bp (28.65%) number of G's = 40,636,557 bp (22.56%) number of N's = 2,679 bp (0%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,080,145 number of insertions = 27,317 mapped reads with insertion percentage = 1.36% number of deletions = 58,764 mapped reads with deletion percentage = 2.96% homopolymer indels = 40.6% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 0.6459X There is a 4.12% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 17841601 0.07158096910017328 0.9404258272793442 chr2 243199373 13518359 0.05558550103663302 0.9590203216615043 chr3 198022430 10938191 0.05523713147040969 0.31154917010830185 chr4 191154276 8391522 0.04389921154575689 0.3788716129317086 chr5 180915260 7802153 0.043126008275918795 0.2943401763443896 chr6 171115067 8693780 0.050806630604889984 0.3299952439939441 chr7 159138663 15527954 0.09757499345083727 1.3449225699669773 chr8 146364022 15077564 0.10301414100249308 0.5519795111042375 chr9 141213431 6679643 0.04730175417945903 0.5441607714628914 chr10 135534747 8709912 0.06426331396774584 0.831978462071853 chr11 135006516 8173869 0.060544255508378574 0.3920339067993497 chr12 133851895 7261723 0.05425192523422997 0.3135114652443225 chr13 115169878 5174128 0.04492605262636468 0.2771473552565423 chr14 107349540 5524828 0.05146578178164527 0.3351441148864605 chr15 102531392 5205703 0.05077179679760907 0.30138653691701495 chr16 90354753 4876580 0.05397148282835768 0.7147214240667734 chr17 81195210 5390271 0.06638656393646866 0.42493819530269566 chr18 78077248 2524625 0.03233496395774605 0.5901975886050397 chr19 59128983 3595633 0.06080999228415615 0.8667959456912183 chr20 63025520 7936339 0.12592262626313913 0.5153153475715121 chr21 48129895 1754335 0.03645000679930841 0.2932959094687755 chr22 51304566 1993031 0.038847049208056844 0.28939283003975935 chrMT 16571 457173 27.588739363949067 16.593918671098685 chrX 155270560 6621862 0.04264724748851295 0.34297658501438405 chrY 59373566 599326 0.010094155368737664 0.8197386355045306