BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714234.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 280,622 number of mapped reads = 21,066 (7.51%) number of supplementary alignments = 422 (0.15%) number of secondary alignments = 0 number of mapped bases = 1,992,811 bp number of sequenced bases = 1,988,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,050 duplication rate = 36.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 12.3017 >>>>>>> ACTG content number of A's = 62,200 bp (3.13%) number of C's = 24,474 bp (1.23%) number of T's = 33,541 bp (1.69%) number of G's = 1,867,600 bp (93.94%) number of N's = 189 bp (0.01%) GC percentage = 95.17% >>>>>>> Mismatches and indels general error rate = 0.0318 number of mismatches = 47,032 number of insertions = 2,321 mapped reads with insertion percentage = 7.6% number of deletions = 1,030 mapped reads with deletion percentage = 4.78% homopolymer indels = 63.56% >>>>>>> Coverage mean coverageData = 0.0006X std coverageData = 2.2792X There is a 0% 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 7116 2.8549577816297597E-5 0.01889723839002792 chr2 243199373 1866911 0.007676463047460242 8.130906182278029 chr3 198022430 6111 3.086014043964616E-5 0.012800555940984368 chr4 191154276 3549 1.8566155433530557E-5 0.010316335983551509 chr5 180915260 4685 2.5896101854536758E-5 0.00832016342876131 chr6 171115067 2908 1.699441230385633E-5 0.006302964932669357 chr7 159138663 7411 4.656944993939028E-5 0.04778982865574096 chr8 146364022 4314 2.947445650270529E-5 0.012286790160707236 chr9 141213431 3603 2.5514570211101237E-5 0.010134551186954832 chr10 135534747 8637 6.372535597827175E-5 0.04105454312771739 chr11 135006516 4193 3.105776020470004E-5 0.019786512386566726 chr12 133851895 5978 4.4661302703260195E-5 0.029757588724401405 chr13 115169878 1190 1.0332562825151209E-5 0.0037643413064574693 chr14 107349540 10002 9.317226697012395E-5 0.06017972879676285 chr15 102531392 3861 3.765675979508793E-5 0.01946578227453164 chr16 90354753 1154 1.2771879305563483E-5 0.006001119697572782 chr17 81195210 3031 3.732978829662489E-5 0.030286660453498454 chr18 78077248 1563 2.0018635902740835E-5 0.005483829421407698 chr19 59128983 924 1.562685426197843E-5 0.005279301879788796 chr20 63025520 7292 1.1569916440197559E-4 0.05542659537957985 chr21 48129895 3733 7.756094211300482E-5 0.03816834360037458 chr22 51304566 342 6.666073347155885E-6 0.002581865393590846 chrMT 16571 397 0.023957516142658862 0.1956834253697406 chrX 155270560 33410 2.1517279257574648E-4 0.0637256497923945 chrY 59373566 496 8.353885970062838E-6 0.0039149222426158965