BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818952.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 = 2,960,051 number of mapped reads = 2,915,681 (98.5%) number of supplementary alignments = 35,016 (1.18%) number of secondary alignments = 0 number of mapped bases = 270,477,386 bp number of sequenced bases = 270,324,483 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,363,105 duplication rate = 38.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4609 >>>>>>> ACTG content number of A's = 78,592,006 bp (29.07%) number of C's = 58,823,627 bp (21.76%) number of T's = 75,529,918 bp (27.94%) number of G's = 57,367,015 bp (21.22%) number of N's = 11,917 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,723,705 number of insertions = 37,523 mapped reads with insertion percentage = 1.25% number of deletions = 83,463 mapped reads with deletion percentage = 2.8% homopolymer indels = 41.59% >>>>>>> Coverage mean coverageData = 0.0874X std coverageData = 0.8935X There is a 3.78% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 32273054 0.12948033537697787 1.5399890260231526 chr2 243199373 23796048 0.09784584436408066 1.3522598806270154 chr3 198022430 18157901 0.09169618310410593 0.5958777265386023 chr4 191154276 17266868 0.09032948862729076 0.6494992464246445 chr5 180915260 13617882 0.07527215780470924 0.5517952733368839 chr6 171115067 14372464 0.08399297766104957 0.6168032331063782 chr7 159138663 13706448 0.08612896289068359 0.7421516978688122 chr8 146364022 17541453 0.11984812087221818 0.7772945608463138 chr9 141213431 10224874 0.0724072344081775 0.9656154612302962 chr10 135534747 13208360 0.097453681010671 1.0764506419281006 chr11 135006516 10433053 0.07727814411565143 0.650548637980866 chr12 133851895 12082495 0.09026764245661222 0.595422315314064 chr13 115169878 4381802 0.03804642390955732 0.3728450394457335 chr14 107349540 6570800 0.06120939130246855 0.5501490173412047 chr15 102531392 8015972 0.078180661001852 0.554576242868647 chr16 90354753 8251449 0.09132279958753249 0.9516788226765719 chr17 81195210 5949308 0.0732716622076598 0.5939829206764635 chr18 78077248 6877746 0.08808899104640573 1.2469459352854615 chr19 59128983 4327057 0.07317996658254718 1.298148303695653 chr20 63025520 5939168 0.09423433555169398 0.6432025023532327 chr21 48129895 3573301 0.07424285883025508 0.5853678814628472 chr22 51304566 3333990 0.06498427449907675 0.5398557483924427 chrMT 16571 46762 2.8219178082191783 3.5984278859072063 chrX 155270560 15737325 0.10135421035384944 0.7666045918621761 chrY 59373566 791806 0.01333600208550721 0.7438205657898481