BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708609.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,648,822 number of mapped reads = 4,393,286 (94.5%) number of supplementary alignments = 132 (0%) number of secondary alignments = 0 number of mapped bases = 219,121,937 bp number of sequenced bases = 219,103,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,155 duplication rate = 0.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7218 >>>>>>> ACTG content number of A's = 67,896,050 bp (30.99%) number of C's = 41,554,836 bp (18.97%) number of T's = 67,406,908 bp (30.76%) number of G's = 42,237,793 bp (19.28%) number of N's = 7,709 bp (0%) GC percentage = 38.24% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 321,687 number of insertions = 13,762 mapped reads with insertion percentage = 0.31% number of deletions = 10,945 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.08% >>>>>>> Coverage mean coverageData = 0.0708X std coverageData = 0.2767X There is a 6.59% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.03% 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 16907652 0.06783394132446315 0.274239183320073 chr2 243199373 19733212 0.0811400611629044 0.29728898311100116 chr3 198022430 16515851 0.0834039406546016 0.29820326616443443 chr4 191154276 17338250 0.090702914749341 0.310682429682315 chr5 180915260 15112472 0.08353342885503412 0.2984361959860856 chr6 171115067 15022585 0.08779229826675637 0.30636844639142347 chr7 159138663 12082717 0.0759257164300796 0.28578228170751346 chr8 146364022 11647581 0.0795795362879547 0.29149929646193706 chr9 141213431 9015973 0.0638464269025515 0.26281636486484156 chr10 135534747 9532681 0.07033385320739928 0.2744962180893936 chr11 135006516 10007947 0.07412936276349802 0.28409268463482534 chr12 133851895 10390077 0.07762368250371053 0.28900560230812605 chr13 115169878 7517961 0.06527714651221564 0.26536265070115206 chr14 107349540 7178385 0.0668692665101313 0.2696525109463501 chr15 102531392 5943288 0.057965544835283225 0.2508905496911092 chr16 90354753 4145217 0.04587713277241763 0.22197236360331887 chr17 81195210 3633805 0.04475393314457836 0.21977799853833072 chr18 78077248 6176775 0.07911107471410878 0.2906035446155923 chr19 59128983 1807282 0.0305650783812737 0.18048149664256485 chr20 63025520 3424615 0.054336957473734446 0.24155037405021063 chr21 48129895 2472615 0.05137378753890903 0.237008419359904 chr22 51304566 1245352 0.024273706944524197 0.16098495708428695 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 11992616 0.07723689539085839 0.287453809377032 chrY 59373566 276878 0.00466332104761907 0.07127123778204907