BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237824.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 = 1,760,358 number of mapped reads = 1,488,110 (84.53%) number of supplementary alignments = 14,720 (0.84%) number of secondary alignments = 0 number of mapped bases = 97,541,075 bp number of sequenced bases = 97,501,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 248,712 duplication rate = 11.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5234 >>>>>>> ACTG content number of A's = 26,500,450 bp (27.18%) number of C's = 18,112,646 bp (18.58%) number of T's = 30,689,775 bp (31.48%) number of G's = 22,048,501 bp (22.61%) number of N's = 150,133 bp (0.15%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 822,072 number of insertions = 6,820 mapped reads with insertion percentage = 0.45% number of deletions = 22,970 mapped reads with deletion percentage = 1.53% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.4074X There is a 1.4% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 8446785 0.03388872198637371 0.5545409103359937 chr2 243199373 5757260 0.02367300511091367 0.4531491655902322 chr3 198022430 5321386 0.02687264265972294 0.31930144546208217 chr4 191154276 6271428 0.03280820147596385 0.3545422216367611 chr5 180915260 5861650 0.032399975546562515 0.3550601061305205 chr6 171115067 4866285 0.028438670453257046 0.35657130442652185 chr7 159138663 6183518 0.038856164073717274 0.5139770146482197 chr8 146364022 4065343 0.02777556222115842 0.38147796585320665 chr9 141213431 4262640 0.030185797270232743 0.36179189121475847 chr10 135534747 4742580 0.034991617315668876 0.4466406232362501 chr11 135006516 4845601 0.0358916083724433 0.39617147865092833 chr12 133851895 3944864 0.029471857682702215 0.3440700289420992 chr13 115169878 4921052 0.04272863777801345 0.41809864881243525 chr14 107349540 3659040 0.03408528811581307 0.37527659547593395 chr15 102531392 2288341 0.022318442726301815 0.28848006558260936 chr16 90354753 3962698 0.0438571062221818 0.42389418820867397 chr17 81195210 2087660 0.025711615254151075 0.30930976348397926 chr18 78077248 2142154 0.027436340993985852 0.5322110100080037 chr19 59128983 2794254 0.047256926438257865 0.5398771007618441 chr20 63025520 2035804 0.03230126463058139 0.35710045078087826 chr21 48129895 1288096 0.026762908998658734 0.3138945502772622 chr22 51304566 973024 0.0189656413817047 0.2658113355924453 chrMT 16571 139139 8.39653611731338 7.064748958070655 chrX 155270560 6413871 0.04130770829962872 0.4089440558635876 chrY 59373566 266602 0.004490247393932849 0.11501385432621794