BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234046.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 = 2,227,657 number of mapped reads = 2,020,686 (90.71%) number of supplementary alignments = 13,956 (0.63%) number of secondary alignments = 0 number of mapped bases = 136,801,214 bp number of sequenced bases = 136,735,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,911 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3743 >>>>>>> ACTG content number of A's = 37,345,639 bp (27.31%) number of C's = 26,216,453 bp (19.17%) number of T's = 42,113,998 bp (30.8%) number of G's = 31,048,118 bp (22.71%) number of N's = 11,277 bp (0.01%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,144,473 number of insertions = 12,510 mapped reads with insertion percentage = 0.61% number of deletions = 38,355 mapped reads with deletion percentage = 1.88% homopolymer indels = 44.47% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 0.4977X There is a 3.81% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 13130457 0.052679736352592675 0.8182863791551407 chr2 243199373 8570629 0.03524116404691553 0.6809197782203579 chr3 198022430 16843620 0.0850591521374624 0.33161863466893776 chr4 191154276 3661678 0.019155616482259597 0.19542213739534142 chr5 180915260 6105170 0.03374602009802821 0.21289655024399456 chr6 171115067 7308507 0.04271106646616923 0.29368513178255484 chr7 159138663 10762560 0.06763007679661101 0.9785882353070473 chr8 146364022 7107539 0.04856069751895722 0.45251775353631596 chr9 141213431 7837682 0.055502383480789445 0.4926144100384462 chr10 135534747 7494741 0.05529756144378238 0.5273763455932238 chr11 135006516 5080420 0.03763092442145533 0.3268813229334941 chr12 133851895 3305017 0.02469159663372715 0.1916394435792594 chr13 115169878 5146631 0.044687300962496464 0.2497250224207773 chr14 107349540 4396453 0.04095455835208982 0.29468584027428196 chr15 102531392 1899670 0.018527691499594583 0.16737269751382386 chr16 90354753 4089963 0.04526560987887378 0.3449456430310079 chr17 81195210 3714720 0.04575048207893052 0.2683005537195936 chr18 78077248 3213064 0.04115237258362385 1.032377422370706 chr19 59128983 4343514 0.07345829032777378 0.5611954518445347 chr20 63025520 3419402 0.05425424494712618 0.28339786256676647 chr21 48129895 3176454 0.06599752606981586 0.3246740343402074 chr22 51304566 1287607 0.025097317848863588 0.17579112559011198 chrMT 16571 28085 1.6948283145253757 1.805662496378176 chrX 155270560 4550642 0.029307822423001503 0.24895868832813148 chrY 59373566 326989 0.005507316168275963 0.14835616196522797