BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053669.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 5,875,392 number of mapped reads = 4,465,777 (76.01%) number of supplementary alignments = 149 (0%) number of secondary alignments = 0 number of mapped bases = 210,458,025 bp number of sequenced bases = 210,417,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 608,654 duplication rate = 10.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7759 >>>>>>> ACTG content number of A's = 63,523,959 bp (30.19%) number of C's = 39,966,852 bp (18.99%) number of T's = 64,653,448 bp (30.73%) number of G's = 42,183,946 bp (20.05%) number of N's = 89,288 bp (0.04%) GC percentage = 39.04% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,455,448 number of insertions = 8,884 mapped reads with insertion percentage = 0.2% number of deletions = 27,507 mapped reads with deletion percentage = 0.61% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.068X std coverageData = 0.4892X There is a 4.07% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 16503380 0.06621199150392489 0.49494955424800974 chr2 243199373 18061162 0.07426483784561402 0.6084174410271961 chr3 198022430 14883330 0.07515981901646192 0.48210799612390487 chr4 191154276 14359939 0.07512224837701251 0.4950505989533025 chr5 180915260 13522951 0.07474743147703516 0.4792344466870357 chr6 171115067 12727496 0.07437975055697463 0.5197018881742265 chr7 159138663 11463265 0.07203318655504853 0.5373436265309808 chr8 146364022 10862528 0.07421583427107517 0.5151170708784998 chr9 141213431 8652528 0.06127269862878695 0.45226399028876907 chr10 135534747 9543366 0.07041268907964982 0.4807274823094056 chr11 135006516 9459383 0.07006612184555595 0.49777621823292223 chr12 133851895 9587354 0.07162658399419747 0.46955315729335506 chr13 115169878 7114671 0.06177544965359779 0.4327315334773883 chr14 107349540 6425730 0.05985801150149316 0.4694615842728552 chr15 102531392 5898968 0.05753328697614873 0.4092534860792099 chr16 90354753 5462463 0.06045573496283035 0.4346780490726011 chr17 81195210 5040960 0.06208445054825278 0.4259459379145924 chr18 78077248 5624848 0.0720420883686884 0.5255629018074381 chr19 59128983 3279670 0.0554663691746567 0.4433595196672697 chr20 63025520 4217615 0.06691916226950606 0.4539775752692159 chr21 48129895 2730267 0.056727050827765156 0.44379638929215115 chr22 51304566 1998055 0.038944974215355414 0.3185026821816286 chrMT 16571 44979 2.7143201979361535 5.703894426079563 chrX 155270560 12539008 0.08075586254084484 0.5301398152160731 chrY 59373566 454109 0.007648336298345294 0.1513178983706961