BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124794.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 494,893 number of mapped reads = 494,132 (99.85%) number of supplementary alignments = 217,614 (43.97%) number of secondary alignments = 0 number of mapped bases = 73,747,835 bp number of sequenced bases = 73,728,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 708,706 duplication rate = 13.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.303 >>>>>>> ACTG content number of A's = 22,287,923 bp (30.23%) number of C's = 14,066,096 bp (19.08%) number of T's = 23,000,281 bp (31.2%) number of G's = 14,373,780 bp (19.5%) number of N's = 0 bp (0%) GC percentage = 38.57% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 525,346 number of insertions = 2,948 mapped reads with insertion percentage = 0.59% number of deletions = 19,133 mapped reads with deletion percentage = 3.83% homopolymer indels = 60.47% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 55.2851X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 471044 0.001889840828119742 1.6182750190710444 chr2 243199373 37551 1.544041809680159E-4 0.07252431336929925 chr3 198022430 38169 1.9275089190653807E-4 0.08479843472468965 chr4 191154276 15430 8.07201404168432E-5 0.009056283941217522 chr5 180915260 16975 9.382845869386585E-5 0.009682916109178439 chr6 171115067 18207 1.0640208556269333E-4 0.015837110210851657 chr7 159138663 26799 1.6840030885517746E-4 0.06598183500122624 chr8 146364022 23894 1.632505015474363E-4 0.02220677841038785 chr9 141213431 12322 8.725798893732707E-5 0.009353671867842825 chr10 135534747 72913292 0.5379675220849455 264.20747107011175 chr11 135006516 19709 1.4598554635688842E-4 0.05787830762224861 chr12 133851895 14376 1.0740228967247718E-4 0.010470532480846412 chr13 115169878 6399 5.556140295642234E-5 0.007438004143501741 chr14 107349540 33873 3.1553931204549176E-4 0.3795953474814195 chr15 102531392 19010 1.8540663136612834E-4 0.07320084443082318 chr16 90354753 22377 2.476571431720919E-4 0.16465414115506452 chr17 81195210 5227 6.437571871542668E-5 0.00805689208594026 chr18 78077248 4775 6.11573809568698E-5 0.008325396817477067 chr19 59128983 16675 2.820106004529116E-4 0.07893482026444883 chr20 63025520 8586 1.3623053010907327E-4 0.012227353813585648 chr21 48129895 3953 8.213190575213182E-5 0.009062293313625935 chr22 51304566 2415 4.7071833723337605E-5 0.006860730133579627 chrMT 16571 129 0.007784684086657414 0.08788676112093537 chrX 155270560 11160 7.187453951347892E-5 0.009387141952407991 chrY 59373566 5488 9.243170605585657E-5 0.009667857076576738