BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708542.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 22,981,238 number of mapped reads = 22,150,289 (96.38%) number of supplementary alignments = 484 (0%) number of secondary alignments = 0 number of mapped bases = 1,104,641,630 bp number of sequenced bases = 1,104,548,477 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,413 duplication rate = 0.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3881 >>>>>>> ACTG content number of A's = 340,493,882 bp (30.83%) number of C's = 210,139,630 bp (19.02%) number of T's = 340,887,543 bp (30.86%) number of G's = 212,582,182 bp (19.25%) number of N's = 445,240 bp (0.04%) GC percentage = 38.27% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,908,450 number of insertions = 57,278 mapped reads with insertion percentage = 0.26% number of deletions = 55,906 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.3568X std coverageData = 0.6619X There is a 27.45% of reference with a coverageData >= 1X There is a 6.53% of reference with a coverageData >= 2X There is a 1.36% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.05% 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 84698823 0.33981388957101133 0.6578403145535504 chr2 243199373 102430566 0.42117939999787746 0.705933401267661 chr3 198022430 85559833 0.43207142241411745 0.7092940633017822 chr4 191154276 92173976 0.48219677806213446 0.7484132359763812 chr5 180915260 79240772 0.4379993815889273 0.7157159882412787 chr6 171115067 74973790 0.43814838350850777 0.7191146356399288 chr7 159138663 63263562 0.3975373476651617 0.6951200935315842 chr8 146364022 61774277 0.4220591656056022 0.7051110185488112 chr9 141213431 46046787 0.32607937271915727 0.6403279429328288 chr10 135534747 47224616 0.3484318010347561 0.6408030365308648 chr11 135006516 49207676 0.3644837112899054 0.6683947662523729 chr12 133851895 51017678 0.3811502108356404 0.6815012537177279 chr13 115169878 46695631 0.40545003442653643 0.7073755024596066 chr14 107349540 35246528 0.32833422481363217 0.6418633315041554 chr15 102531392 29595916 0.28865224028168857 0.606524957298073 chr16 90354753 19816256 0.21931614377829134 0.5195259573792033 chr17 81195210 17472951 0.21519682010798422 0.518766407576769 chr18 78077248 33492364 0.4289644532553197 0.7113432555539105 chr19 59128983 7638307 0.12918042239962085 0.3905438315314153 chr20 63025520 16867115 0.26762357533900555 0.574968587317351 chr21 48129895 14226302 0.2955814052783618 0.6293036248294531 chr22 51304566 5580595 0.1087738467566415 0.36463727005430774 chrMT 16571 1068 0.06444994267093114 0.26034419468457315 chrX 155270560 35357700 0.2277167030247073 0.5019400175842581 chrY 59373566 5038541 0.08486168743848062 0.3264950660942984