BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085026.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 = 2,176,489 number of mapped reads = 1,936,076 (88.95%) number of supplementary alignments = 11,325 (0.52%) number of secondary alignments = 0 number of mapped bases = 129,099,776 bp number of sequenced bases = 129,054,029 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,868 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9537 >>>>>>> ACTG content number of A's = 35,611,161 bp (27.59%) number of C's = 24,821,896 bp (19.23%) number of T's = 39,573,542 bp (30.66%) number of G's = 29,041,155 bp (22.5%) number of N's = 6,275 bp (0%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,100,404 number of insertions = 8,995 mapped reads with insertion percentage = 0.46% number of deletions = 27,042 mapped reads with deletion percentage = 1.38% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.3369X There is a 3.62% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10963260 0.043984885397737886 0.4620784968737163 chr2 243199373 12383916 0.050920838517128905 0.47543075164957294 chr3 198022430 7830614 0.039544075890796816 0.22349513704579152 chr4 191154276 7660385 0.04007435857725725 0.22745269392725348 chr5 180915260 6413897 0.03545249306222151 0.2109089850426547 chr6 171115067 9001432 0.05260455527273937 0.3376952128710851 chr7 159138663 11365181 0.07141684356114014 0.3878648888412686 chr8 146364022 6637130 0.04534673145289762 0.5194499661428487 chr9 141213431 4269624 0.030235254322232282 0.32949299989877723 chr10 135534747 9457009 0.06977553143623015 0.4139276613251592 chr11 135006516 5358160 0.03968815845895912 0.33557089953061997 chr12 133851895 5418004 0.040477603996566504 0.2323768862707115 chr13 115169878 2698147 0.023427540663019546 0.16902222394186953 chr14 107349540 4281647 0.03988509871583986 0.24092226535287836 chr15 102531392 2360119 0.023018501494644683 0.17262653112208667 chr16 90354753 3512890 0.038878862299584836 0.23625131450677936 chr17 81195210 2293636 0.02824841514665705 0.21550490769292097 chr18 78077248 3023164 0.03872016595666897 0.5420815031707512 chr19 59128983 2164724 0.03661020180238852 0.3707140544313806 chr20 63025520 3074308 0.04877878040514382 0.25240892435013373 chr21 48129895 1471998 0.030583860613034787 0.20963454263126546 chr22 51304566 944338 0.0184065098611301 0.14886622387404866 chrMT 16571 11144 0.6725001508659707 0.8889745111852194 chrX 155270560 6244015 0.040213772655936834 0.26121445923546255 chrY 59373566 261034 0.004396468286914079 0.09126373610625964