BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004093.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,707,655 number of mapped reads = 3,395,625 (91.58%) number of supplementary alignments = 33,579 (0.91%) number of secondary alignments = 0 number of mapped bases = 225,206,248 bp number of sequenced bases = 225,101,085 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,289 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.779 >>>>>>> ACTG content number of A's = 61,471,568 bp (27.31%) number of C's = 42,861,316 bp (19.04%) number of T's = 69,112,307 bp (30.7%) number of G's = 51,608,637 bp (22.93%) number of N's = 47,257 bp (0.02%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,874,789 number of insertions = 17,657 mapped reads with insertion percentage = 0.52% number of deletions = 64,349 mapped reads with deletion percentage = 1.87% homopolymer indels = 46.01% >>>>>>> Coverage mean coverageData = 0.0727X std coverageData = 0.6205X There is a 6.01% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15509732 0.06222544978132672 1.200180272138931 chr2 243199373 20875449 0.08583677146240011 0.7648833811141006 chr3 198022430 14065038 0.0710274992585436 0.3100259134910971 chr4 191154276 17011101 0.08899147513707724 0.36223707622039686 chr5 180915260 10845765 0.059949420518755576 0.29452038855004753 chr6 171115067 12913341 0.07546583259088459 0.3773381292652006 chr7 159138663 14056836 0.08833074084579937 0.988828127671565 chr8 146364022 12609543 0.08615193015124988 0.6378497096895094 chr9 141213431 9841981 0.06969578552340393 0.5614010909862397 chr10 135534747 11635169 0.08584639184813618 0.5279604937121336 chr11 135006516 9797160 0.07256805293753377 0.5183218127782946 chr12 133851895 8854236 0.066149500535648 0.32186589915975305 chr13 115169878 7043647 0.06115876062662843 0.28910012140513164 chr14 107349540 6837344 0.06369234558434066 0.36054648178848714 chr15 102531392 5510135 0.05374095574553401 0.2808243191710352 chr16 90354753 4654937 0.0515184519402095 0.35133974250236544 chr17 81195210 6410017 0.0789457530807544 0.37096810523057266 chr18 78077248 5960659 0.07634309805591509 1.2257178055665103 chr19 59128983 4780452 0.08084786440517673 0.7980436924922137 chr20 63025520 4410715 0.06998300053692535 0.3293211866344205 chr21 48129895 3305213 0.06867276564804474 0.33995264895251365 chr22 51304566 2547548 0.04965538544853883 0.2576833193155831 chrMT 16571 171616 10.356405769114719 6.401930909232671 chrX 155270560 14987616 0.09652580630867821 0.43263950676352775 chrY 59373566 570998 0.009617040687770043 0.17616743244140062