BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081113.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 = 2,450,556 number of mapped reads = 2,254,754 (92.01%) number of supplementary alignments = 13,789 (0.56%) number of secondary alignments = 0 number of mapped bases = 152,240,582 bp number of sequenced bases = 152,182,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,867 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6145 >>>>>>> ACTG content number of A's = 41,866,650 bp (27.51%) number of C's = 29,904,356 bp (19.65%) number of T's = 46,162,172 bp (30.33%) number of G's = 34,247,846 bp (22.5%) number of N's = 1,648 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,331,594 number of insertions = 11,571 mapped reads with insertion percentage = 0.51% number of deletions = 32,470 mapped reads with deletion percentage = 1.43% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.3932X There is a 4.05% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12894304 0.05173228435005584 0.5258621480801406 chr2 243199373 10267904 0.04222010884871812 0.4414450187844345 chr3 198022430 12604156 0.06365014306712628 0.29603233964904846 chr4 191154276 8864899 0.04637562489054652 0.2862003580836623 chr5 180915260 8284019 0.0457894983540913 0.2496035630754131 chr6 171115067 12294895 0.07185162134202945 0.4416826879468749 chr7 159138663 7711333 0.04845669087970156 0.5460487709076595 chr8 146364022 11422467 0.07804149437762786 0.44911180840410025 chr9 141213431 7425396 0.052582788672559055 0.4862119559856758 chr10 135534747 7052613 0.05203546069260011 0.3739958401574432 chr11 135006516 6784374 0.050252196716194054 0.3420154590819399 chr12 133851895 7454720 0.055693794996327844 0.28844478259924805 chr13 115169878 3821126 0.03317817181329306 0.21160638669287873 chr14 107349540 4332602 0.040359763069315435 0.3052248257306753 chr15 102531392 3920105 0.038233217393556895 0.22986741928402035 chr16 90354753 4063099 0.04496829292422503 0.2984741890469762 chr17 81195210 3808538 0.04690594432848933 0.267918452702573 chr18 78077248 3910037 0.050079083217687184 0.8624068911712963 chr19 59128983 3462249 0.05855417807541185 0.43302486847301125 chr20 63025520 2646250 0.04198696020278769 0.2575451098145871 chr21 48129895 2839460 0.058995765521616034 0.36044261726386373 chr22 51304566 1565709 0.030517927000883315 0.20292401969407903 chrMT 16571 116576 7.0349405588075555 4.8987521928292574 chrX 155270560 4282309 0.027579658371812404 0.2339404290527726 chrY 59373566 411442 0.006929716837287489 0.1787907854949923