BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504415.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,241,719 number of mapped reads = 1,897,583 (84.65%) number of secondary alignments = 0 number of mapped bases = 60,716,490 bp number of sequenced bases = 60,716,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,311 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.3772 >>>>>>> ACTG content number of A's = 17,551,426 bp (28.91%) number of C's = 12,237,019 bp (20.15%) number of T's = 18,688,118 bp (30.78%) number of G's = 12,239,780 bp (20.16%) number of N's = 147 bp (0%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 28,695 >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.2429X There is a 1.51% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 5855356 0.023491841169775863 0.4085068305361305 chr2 243199373 5139370 0.021132332442320892 0.17928106238994374 chr3 198022430 4174684 0.02108187441190374 0.17811709105310625 chr4 191154276 3898544 0.020394751723994915 0.17984048307239903 chr5 180915260 4091234 0.022614090154694524 0.22346369356702053 chr6 171115067 3879144 0.022669797978689978 0.21928263701008205 chr7 159138663 4276824 0.02687482676664187 0.3406381490452489 chr8 146364022 3913880 0.026740724575059847 0.3465212771426893 chr9 141213431 2366614 0.016759128244678085 0.1647648121064667 chr10 135534747 2689226 0.019841598258194263 0.2146508447928378 chr11 135006516 3208196 0.023763267841087017 0.22637633135413673 chr12 133851895 3175930 0.023727194897016586 0.3262391898203313 chr13 115169878 2029980 0.017625962927563403 0.24374079724493386 chr14 107349540 1976824 0.018414834381218586 0.24494720043667517 chr15 102531392 1798104 0.01753710707448505 0.29102486185673226 chr16 90354753 1368204 0.015142579162382304 0.16804424152242523 chr17 81195210 978600 0.01205243511285949 0.12546940896185388 chr18 78077248 1675952 0.021465305744382795 0.21965369410574764 chr19 59128983 594162 0.010048574655850245 0.11216398517679055 chr20 63025520 964734 0.015307037530194119 0.15808481825194226 chr21 48129895 707644 0.014702795424756276 0.1600640289234585 chr22 51304566 477268 0.009302641796053786 0.11853721745200907 chrMT 16571 0 0.0 0.0 chrX 155270560 734338 0.0047294091036961545 0.07473798232569988 chrY 59373566 741678 0.012491720642145699 0.15291220435872685