BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818934.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,732,258 number of mapped reads = 1,706,451 (98.51%) number of supplementary alignments = 22,636 (1.31%) number of secondary alignments = 0 number of mapped bases = 158,011,173 bp number of sequenced bases = 157,920,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 611,819 duplication rate = 30.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4478 >>>>>>> ACTG content number of A's = 44,351,541 bp (28.08%) number of C's = 32,448,966 bp (20.55%) number of T's = 46,138,834 bp (29.22%) number of G's = 34,974,319 bp (22.15%) number of N's = 6,525 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 966,086 number of insertions = 18,642 mapped reads with insertion percentage = 1.06% number of deletions = 49,381 mapped reads with deletion percentage = 2.83% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.5554X There is a 2.7% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 18580151 0.07454405098553396 0.8723589819290721 chr2 243199373 14276312 0.05870209213080496 0.8659250865349146 chr3 198022430 10609315 0.05357632971174023 0.38843291554286574 chr4 191154276 9691007 0.05069730692291707 0.412856385609025 chr5 180915260 8335948 0.04607653328967385 0.37730273144567694 chr6 171115067 8041145 0.04699261813104979 0.3895939959895109 chr7 159138663 8175557 0.05137379468872376 0.473608376732451 chr8 146364022 10674202 0.07292913828235739 0.5001551378759567 chr9 141213431 5986779 0.042395252049360656 0.6052419776714633 chr10 135534747 7492079 0.055277920723901156 0.648827378367536 chr11 135006516 5989152 0.044361947685547264 0.41088091103116886 chr12 133851895 7072186 0.05283590493806606 0.3941356408820638 chr13 115169878 2565208 0.022273254470235697 0.24545832395306022 chr14 107349540 3986113 0.03713209204249967 0.36060052047938385 chr15 102531392 4639393 0.04524851276767997 0.35769283526741574 chr16 90354753 4945381 0.054732936960161904 0.6367246778031627 chr17 81195210 3330077 0.041013219868511946 0.37527443212351497 chr18 78077248 3891217 0.04983803988583204 0.8064110386594576 chr19 59128983 2493250 0.04216629262843909 0.7760073433167113 chr20 63025520 3502581 0.0555740119240587 0.41660066134895885 chr21 48129895 2147778 0.044624614285985874 0.3769843986792469 chr22 51304566 1977010 0.0385347768071949 0.36468934912725576 chrMT 16571 15778 0.9521453141029509 1.525431904834425 chrX 155270560 9098658 0.058598732431956194 0.47887137311961747 chrY 59373566 494896 0.008335291836774634 0.4965323009371725