BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714178.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 = 1,715,858 number of mapped reads = 1,620,824 (94.46%) number of supplementary alignments = 106,313 (6.2%) number of secondary alignments = 0 number of mapped bases = 204,895,008 bp number of sequenced bases = 200,741,783 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,544,786 duplication rate = 48.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2986 >>>>>>> ACTG content number of A's = 58,510,859 bp (29.15%) number of C's = 41,437,926 bp (20.64%) number of T's = 55,142,246 bp (27.47%) number of G's = 45,649,201 bp (22.74%) number of N's = 1,551 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0379 number of mismatches = 7,221,233 number of insertions = 175,078 mapped reads with insertion percentage = 10.5% number of deletions = 644,727 mapped reads with deletion percentage = 37.91% homopolymer indels = 27.94% >>>>>>> Coverage mean coverageData = 0.0662X std coverageData = 11.921X There is a 0.1% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12659230 0.050789161323694355 10.347659191960378 chr2 243199373 20631601 0.08483410440371489 17.38594699064038 chr3 198022430 12184170 0.06152924191466593 8.433799359374875 chr4 191154276 14138217 0.07396233710199608 12.132562571598811 chr5 180915260 12928357 0.07146084304883955 11.813400931756505 chr6 171115067 14299148 0.08356451743667903 17.027480000548042 chr7 159138663 8955639 0.05627569586907991 9.475245090587155 chr8 146364022 9487892 0.06482393603531884 8.966773814308311 chr9 141213431 7332350 0.051923885342039455 7.523274478943029 chr10 135534747 9997962 0.07376678100118489 13.046463632209049 chr11 135006516 9004823 0.06669917324583059 10.319043239979525 chr12 133851895 6262162 0.046784261067054744 6.0035424688974715 chr13 115169878 4739646 0.04115352106216523 4.6987523817645585 chr14 107349540 4741829 0.04417186137919175 5.954027594293634 chr15 102531392 4382017 0.04273829618932707 5.2617069119701645 chr16 90354753 3220095 0.0356383576191061 4.620985635576071 chr17 81195210 1880844 0.023164469923779987 3.1282123515285494 chr18 78077248 5143318 0.06587473472425667 8.719031065468073 chr19 59128983 660614 0.011172422837037465 1.3759878138851336 chr20 63025520 3041886 0.04826435386808391 8.178600785115004 chr21 48129895 2046794 0.04252645886719678 6.700804144753564 chr22 51304566 704731 0.013736223789516121 1.7827123821899538 chrMT 16571 6027 0.3637076820952266 2.54554929843664 chrX 155270560 35534044 0.22885242379495507 27.9690570238587 chrY 59373566 911612 0.015353836082542188 2.473302971355351