BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716134.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 = 469,968 number of mapped reads = 430,923 (91.69%) number of supplementary alignments = 939 (0.2%) number of secondary alignments = 0 number of mapped bases = 24,901,775 bp number of sequenced bases = 24,894,027 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,505 duplication rate = 1.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.073 >>>>>>> ACTG content number of A's = 5,896,643 bp (23.69%) number of C's = 4,377,878 bp (17.59%) number of T's = 8,301,123 bp (33.35%) number of G's = 6,318,114 bp (25.38%) number of N's = 269 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 123,071 number of insertions = 1,419 mapped reads with insertion percentage = 0.33% number of deletions = 4,967 mapped reads with deletion percentage = 1.14% homopolymer indels = 45.8% >>>>>>> Coverage mean coverageData = 0.008X std coverageData = 0.1056X There is a 0.77% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 2947174 0.01182413904597654 0.14001549117581288 chr2 243199373 2551427 0.010491092014451862 0.1394913279389667 chr3 198022430 1559939 0.007877587402598786 0.09185454952331396 chr4 191154276 1116249 0.005839518860671472 0.08008069330810395 chr5 180915260 1855089 0.01025391114049749 0.10421349587854012 chr6 171115067 994155 0.005809862436017981 0.08269395844497322 chr7 159138663 1331932 0.008369631709171769 0.12740970134302984 chr8 146364022 1104351 0.007545235399448097 0.09638188608391778 chr9 141213431 706233 0.005001174427948005 0.08735086867214636 chr10 135534747 1172736 0.008652659380402281 0.12213885877693696 chr11 135006516 1100638 0.008152480581011364 0.10390634476440033 chr12 133851895 1056817 0.007895420531775063 0.09180238042167747 chr13 115169878 764840 0.006640972564024076 0.08374105764098931 chr14 107349540 511202 0.004762032515463038 0.0723386920388633 chr15 102531392 978917 0.009547485710522685 0.1006316411825361 chr16 90354753 747482 0.008272746869221147 0.09821969340450523 chr17 81195210 920147 0.0113325281134195 0.11214588227142526 chr18 78077248 830419 0.010635864112423635 0.1491246611603889 chr19 59128983 419597 0.007096299965111864 0.106421962831672 chr20 63025520 633622 0.010053419630651202 0.10333212302162374 chr21 48129895 314093 0.006525944010474155 0.0837526862181781 chr22 51304566 269377 0.005250546315897107 0.07480944698578142 chrMT 16571 3670 0.22147124494599 0.5552673220972854 chrX 155270560 957368 0.006165805030908628 0.08629712010029089 chrY 59373566 54301 9.145652460894803E-4 0.03326650440907298