BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714128.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 1,199,008 number of mapped reads = 76,256 (6.36%) number of supplementary alignments = 1,916 (0.16%) number of secondary alignments = 0 number of mapped bases = 6,583,430 bp number of sequenced bases = 6,519,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,874 duplication rate = 33.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 29.3965 >>>>>>> ACTG content number of A's = 748,235 bp (11.48%) number of C's = 471,492 bp (7.23%) number of T's = 623,113 bp (9.56%) number of G's = 4,676,468 bp (71.73%) number of N's = 196 bp (0%) GC percentage = 78.96% >>>>>>> Mismatches and indels general error rate = 0.0336 number of mismatches = 181,664 number of insertions = 7,026 mapped reads with insertion percentage = 7.08% number of deletions = 9,096 mapped reads with deletion percentage = 11.49% homopolymer indels = 39.22% >>>>>>> Coverage mean coverageData = 0.0021X std coverageData = 4.9189X There is a 0.01% of reference with a coverageData >= 1X There is a 0% 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 113155 4.539808147559239E-4 0.1645784748984684 chr2 243199373 4444293 0.018274278198899797 17.528628491923048 chr3 198022430 113063 5.709605724967622E-4 0.1868978513125645 chr4 191154276 111584 5.837379227655885E-4 0.1917788846843949 chr5 180915260 169264 9.355982463834173E-4 0.22949315554511449 chr6 171115067 82624 4.828563693926497E-4 0.17804259792566 chr7 159138663 100697 6.327626366950186E-4 0.4982535480465854 chr8 146364022 151610 0.0010358419912784305 0.3289474046081043 chr9 141213431 63892 4.5244988063493764E-4 0.14595784000189477 chr10 135534747 65284 4.816772189053483E-4 0.1696223608254382 chr11 135006516 56661 4.196908540325565E-4 0.12612963777809516 chr12 133851895 48359 3.612873766187621E-4 0.11075790069562196 chr13 115169878 45479 3.948862392647494E-4 0.12369507805637348 chr14 107349540 71920 6.699609518587597E-4 0.20997051267560302 chr15 102531392 17062 1.664075720341337E-4 0.03949033152983678 chr16 90354753 56690 6.274158040142061E-4 0.15018662568716845 chr17 81195210 45105 5.555130653643239E-4 0.1877918839949233 chr18 78077248 52247 6.69170614210173E-4 0.16159802472416696 chr19 59128983 7101 1.2009338973410045E-4 0.026381611678887317 chr20 63025520 12562 1.9931608656303034E-4 0.04729163801964478 chr21 48129895 23236 4.8277686872161263E-4 0.10644411168477776 chr22 51304566 10088 1.9662967229856304E-4 0.04890001707931274 chrMT 16571 14272 0.8612636533703458 7.874411944070258 chrX 155270560 690703 0.004448383518421007 0.6222032870947076 chrY 59373566 16479 2.77547755848116E-4 0.12628157757742295