BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083622.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,702,217 number of mapped reads = 1,552,031 (91.18%) number of supplementary alignments = 14,587 (0.86%) number of secondary alignments = 0 number of mapped bases = 103,266,559 bp number of sequenced bases = 103,226,943 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,064 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7427 >>>>>>> ACTG content number of A's = 27,932,358 bp (27.06%) number of C's = 19,180,934 bp (18.58%) number of T's = 32,591,427 bp (31.57%) number of G's = 23,517,190 bp (22.78%) number of N's = 5,034 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 753,046 number of insertions = 7,652 mapped reads with insertion percentage = 0.49% number of deletions = 24,125 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 0.3234X There is a 2.92% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8934766 0.03584651450076026 0.6445738971998137 chr2 243199373 9739576 0.04004770193219207 0.376381513518667 chr3 198022430 8682871 0.04384791662237455 0.2349999872516379 chr4 191154276 5084856 0.02660079652102577 0.18648170799485483 chr5 180915260 4827192 0.02668206098258378 0.18149206673935667 chr6 171115067 7379356 0.04312510949138103 0.29904724908564584 chr7 159138663 6989159 0.04391867361610296 0.5496893635454012 chr8 146364022 6297978 0.04302954998052732 0.3358779244283069 chr9 141213431 4510006 0.03193751449888644 0.23857604316490832 chr10 135534747 4474192 0.033011401865825594 0.2571982802383177 chr11 135006516 4565227 0.03381486416551924 0.2461360312091701 chr12 133851895 3747451 0.027996996232290922 0.18701135197658214 chr13 115169878 3377348 0.029324924699494777 0.1903109648067563 chr14 107349540 2168895 0.02020404558789912 0.16018048636518092 chr15 102531392 2811721 0.027423025720747066 0.18809078949266136 chr16 90354753 2946123 0.032606176235133975 0.21165077146883432 chr17 81195210 2258283 0.027813007688507734 0.19845659317787498 chr18 78077248 2743149 0.035133781866901866 0.3789862101186996 chr19 59128983 3032585 0.05128762319487213 0.44133033082647855 chr20 63025520 1688913 0.026797287828803317 0.1848412669077881 chr21 48129895 1815655 0.03772405902817781 0.22060256976599352 chr22 51304566 686363 0.013378204973023259 0.12627691799238547 chrMT 16571 33805 2.040009655422123 1.8267808663606602 chrX 155270560 4256944 0.027416298363321417 0.19382577377683724 chrY 59373566 214145 0.0036067397400385216 0.08537101474962985