BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082692.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 = 3,574,281 number of mapped reads = 3,286,643 (91.95%) number of supplementary alignments = 13,954 (0.39%) number of secondary alignments = 0 number of mapped bases = 217,002,568 bp number of sequenced bases = 216,919,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,413 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5133 >>>>>>> ACTG content number of A's = 59,447,447 bp (27.41%) number of C's = 37,069,051 bp (17.09%) number of T's = 72,487,054 bp (33.42%) number of G's = 47,859,780 bp (22.06%) number of N's = 56,382 bp (0.03%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,976,087 number of insertions = 19,815 mapped reads with insertion percentage = 0.6% number of deletions = 51,933 mapped reads with deletion percentage = 1.56% homopolymer indels = 49.1% >>>>>>> Coverage mean coverageData = 0.0701X std coverageData = 0.5532X There is a 5.7% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 21440470 0.08601972550351239 0.8760575663627092 chr2 243199373 20433469 0.08401941480334327 0.7684606025261362 chr3 198022430 19287531 0.09740073889609374 0.37163944035424334 chr4 191154276 11793098 0.06169413652038838 0.30362283174179616 chr5 180915260 14020367 0.07749687339807598 0.33327395180866165 chr6 171115067 14000121 0.08181699744768822 0.520324217698354 chr7 159138663 9352006 0.05876639795572494 0.8237450245857052 chr8 146364022 15796272 0.1079245553938112 0.5496898527374163 chr9 141213431 7252924 0.05136143176069421 0.6099272198469436 chr10 135534747 9264724 0.0683568177539004 0.4793055885159897 chr11 135006516 9184900 0.06803301256955627 0.49156341402352377 chr12 133851895 7720308 0.05767798804790922 0.2888123029455083 chr13 115169878 5238160 0.045482031334616854 0.24680759825060902 chr14 107349540 4912326 0.0457601029310419 0.2980759006687804 chr15 102531392 4156019 0.04053411271349949 0.23373598472910329 chr16 90354753 7193426 0.07961314442417877 0.38279765405731825 chr17 81195210 5563070 0.06851475598129496 0.4408866097297604 chr18 78077248 5597622 0.07169338243069223 1.1457038466763658 chr19 59128983 2992854 0.050615685373786995 0.6619848803082434 chr20 63025520 5175756 0.08212159138076132 0.3602230900869037 chr21 48129895 3962477 0.08232881039944093 0.35521697787928613 chr22 51304566 2756285 0.05372397068908058 0.2712711112737468 chrMT 16571 2311 0.13946050328887816 0.3837809776535651 chrX 155270560 9517763 0.061297924088120764 0.37402213448516364 chrY 59373566 388309 0.006540099006349055 0.13565953396170533