BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524442.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,209,083 number of mapped reads = 2,986,929 (93.08%) number of supplementary alignments = 6,778 (0.21%) number of secondary alignments = 0 number of mapped bases = 175,568,543 bp number of sequenced bases = 175,508,967 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,336 duplication rate = 5.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7245 >>>>>>> ACTG content number of A's = 45,450,225 bp (25.9%) number of C's = 31,410,313 bp (17.9%) number of T's = 54,700,821 bp (31.17%) number of G's = 43,943,984 bp (25.04%) number of N's = 3,624 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 807,950 number of insertions = 13,555 mapped reads with insertion percentage = 0.45% number of deletions = 34,561 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.8% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.4755X There is a 4.56% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% 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 17303149 0.06942068561586452 0.9169126221388872 chr2 243199373 13890358 0.057115106131461944 0.5121887614304295 chr3 198022430 9631178 0.04863680341666345 0.267428022442535 chr4 191154276 9965382 0.0521326658682749 0.3417782780680547 chr5 180915260 9782277 0.05407104408992365 0.282651066697549 chr6 171115067 7555498 0.04415448699207768 0.3643977260802492 chr7 159138663 8687969 0.0545937036055154 0.6638270891143219 chr8 146364022 16241012 0.11096314366108359 0.5018585611883207 chr9 141213431 7423383 0.05256853365456435 0.41040674564830937 chr10 135534747 9162630 0.06760354966391018 0.5027096833999365 chr11 135006516 6069838 0.04495959291327835 0.4604710605867266 chr12 133851895 8138838 0.060804802203211245 0.2981543256826934 chr13 115169878 3889563 0.03377239836965009 0.22408484325292938 chr14 107349540 4140717 0.03857228452026902 0.24546707377987706 chr15 102531392 4654576 0.04539659424500937 0.27929286890208543 chr16 90354753 5484572 0.060700426019647244 0.3233238627218327 chr17 81195210 6031069 0.07427863047586182 0.35401876455911985 chr18 78077248 4162544 0.05331314956182882 0.7601653118433591 chr19 59128983 3424229 0.05791117699419927 0.6225914666332207 chr20 63025520 4966340 0.07879887385300431 0.3480980845331888 chr21 48129895 2422825 0.05033929535894479 0.30661670697773774 chr22 51304566 1417656 0.027632160459168487 0.19981057167075655 chrMT 16571 14302 0.8630740450184057 1.0859241487268676 chrX 155270560 10559728 0.06800856517809944 0.3689280355706313 chrY 59373566 548910 0.009245023281909664 0.2357052175475345