BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714227.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 = 234,302 number of mapped reads = 35,812 (15.28%) number of supplementary alignments = 808 (0.34%) number of secondary alignments = 0 number of mapped bases = 3,597,394 bp number of sequenced bases = 3,587,506 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,881 duplication rate = 34.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.4185 >>>>>>> ACTG content number of A's = 113,672 bp (3.17%) number of C's = 47,572 bp (1.33%) number of T's = 67,198 bp (1.87%) number of G's = 3,359,010 bp (93.63%) number of N's = 54 bp (0%) GC percentage = 94.96% >>>>>>> Mismatches and indels general error rate = 0.0333 number of mismatches = 90,548 number of insertions = 4,156 mapped reads with insertion percentage = 7.9% number of deletions = 2,004 mapped reads with deletion percentage = 5.33% homopolymer indels = 62.45% >>>>>>> Coverage mean coverageData = 0.0012X std coverageData = 4.2438X 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 46154 1.8517105319468792E-4 0.4779272138094017 chr2 243199373 3354727 0.013794143293288836 15.125794418660684 chr3 198022430 3100 1.5654792237424822E-5 0.005376390174079441 chr4 191154276 4527 2.3682441715298068E-5 0.011015974164816327 chr5 180915260 5788 3.1992878875999736E-5 0.009691876429204086 chr6 171115067 4201 2.4550731117090934E-5 0.010240051879627702 chr7 159138663 7507 4.717269743556913E-5 0.04295140133521282 chr8 146364022 3013 2.0585660046975206E-5 0.008009662522933567 chr9 141213431 1921 1.3603521891625166E-5 0.006005479950307475 chr10 135534747 41699 3.0766280177584276E-4 0.6116526441053168 chr11 135006516 2713 2.009532636187723E-5 0.015096102154542356 chr12 133851895 5690 4.250967085673311E-5 0.030151161368365643 chr13 115169878 1316 1.1426598888990748E-5 0.004934218607461503 chr14 107349540 4895 4.5598704940887496E-5 0.039904930076320164 chr15 102531392 3620 3.530626015493869E-5 0.01500270806390177 chr16 90354753 12592 1.3936178874840154E-4 0.0960733476935186 chr17 81195210 5217 6.425255874084197E-5 0.0645925701503867 chr18 78077248 861 1.1027540314945527E-5 0.0035009956072057343 chr19 59128983 2912 4.924826797714414E-5 0.02114805368617423 chr20 63025520 838 1.3296201284812883E-5 0.004572962611438865 chr21 48129895 589 1.2237716288389992E-5 0.004623796470968853 chr22 51304566 573 1.1168596572866438E-5 0.004264433273966506 chrMT 16571 1829 0.11037354414338302 0.6832031776286085 chrX 155270560 80372 5.176254919155312E-4 0.0987310948301535 chrY 59373566 740 1.246345890694859E-5 0.0053240767123806385