BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068076.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 = 4,439,925 number of mapped reads = 4,171,147 (93.95%) number of supplementary alignments = 30,426 (0.69%) number of secondary alignments = 0 number of mapped bases = 267,426,434 bp number of sequenced bases = 267,315,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 570,762 duplication rate = 11.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6127 >>>>>>> ACTG content number of A's = 69,074,169 bp (25.84%) number of C's = 47,699,820 bp (17.84%) number of T's = 87,681,861 bp (32.8%) number of G's = 62,830,037 bp (23.5%) number of N's = 29,621 bp (0.01%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,518,200 number of insertions = 16,606 mapped reads with insertion percentage = 0.39% number of deletions = 63,108 mapped reads with deletion percentage = 1.5% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 0.0864X std coverageData = 0.9684X There is a 6.17% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 31335619 0.12571932167823968 2.2280397052492757 chr2 243199373 27973731 0.11502386151299823 1.521968747489843 chr3 198022430 18379244 0.09281395041965701 0.40634290163729025 chr4 191154276 13719384 0.0717712639606346 0.3786501525469949 chr5 180915260 12754465 0.07049966376523462 0.35821617173276604 chr6 171115067 14734964 0.08611143517829438 0.5644971790615826 chr7 159138663 22707852 0.1426922381520825 1.407636322585399 chr8 146364022 11742234 0.08022623209957977 0.7844241647356172 chr9 141213431 11452360 0.0810996512081064 0.6294251102355671 chr10 135534747 7677098 0.056643024537464184 0.5048068609840768 chr11 135006516 13036381 0.0965611245015759 0.6088572013742584 chr12 133851895 9107791 0.06804379571914167 0.3831421974802669 chr13 115169878 8087693 0.07022403027986189 0.40286515324478345 chr14 107349540 5692897 0.053031405630615654 0.35999261843693303 chr15 102531392 7006244 0.0683326722024802 0.38915386578890243 chr16 90354753 7159562 0.07923835506473025 0.4169776591142235 chr17 81195210 6934911 0.08541034625072094 0.43799792507501034 chr18 78077248 7930356 0.10157063937499436 1.2029619528652025 chr19 59128983 5469416 0.09249974754343399 1.485727931496292 chr20 63025520 3409271 0.05409350053756002 0.34748658216353223 chr21 48129895 3055454 0.06348349606829601 0.35768334869106366 chr22 51304566 2980965 0.058103307997966494 0.3135844438165061 chrMT 16571 270138 16.301852634119847 9.354194431620439 chrX 155270560 14197345 0.09143616793808176 0.5208617672261296 chrY 59373566 611059 0.010291768562460944 0.35416606093354486