BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472509.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,447,514 number of mapped reads = 16,229,773 (98.68%) number of supplementary alignments = 55,688 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,143,190 number of mapped paired reads (second in pair) = 8,086,583 number of mapped paired reads (both in pair) = 16,118,900 number of mapped paired reads (singletons) = 110,873 number of mapped bases = 1,597,430,338 bp number of sequenced bases = 1,597,231,479 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,999,205 duplication rate = 44.83% >>>>>>> Insert size mean insert size = 25,974.0122 std insert size = 1,596,828.4555 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 55.0168 >>>>>>> ACTG content number of A's = 442,708,287 bp (27.72%) number of C's = 358,185,327 bp (22.43%) number of T's = 440,421,360 bp (27.57%) number of G's = 355,668,949 bp (22.27%) number of N's = 247,556 bp (0.02%) GC percentage = 44.69% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,071,632 number of insertions = 87,789 mapped reads with insertion percentage = 0.53% number of deletions = 79,264 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.516X std coverageData = 17.7505X There is a 5.1% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187853488 0.7536730991735423 24.073745365493725 chr2 243199373 124524571 0.5120266942464526 18.620457859121995 chr3 198022430 177154522 0.8946184631710661 23.492416221452384 chr4 191154276 60913257 0.3186601852422072 10.499206790431488 chr5 180915260 83747267 0.46290880603438317 15.12094841802753 chr6 171115067 94015707 0.5494297413330645 14.600019603369411 chr7 159138663 64779028 0.40706027547812185 13.59565488152838 chr8 146364022 55730087 0.3807635663359948 11.746285927720923 chr9 141213431 77249948 0.5470439139744434 14.995640894950812 chr10 135534747 43840319 0.3234618425930289 13.292160849994522 chr11 135006516 74073130 0.5486633696998744 20.139853650492288 chr12 133851895 105794915 0.7903878760924528 27.8991978525355 chr13 115169878 41364205 0.3591581906512048 12.653586682109854 chr14 107349540 33159996 0.30889742051992025 10.505626240434964 chr15 102531392 46884582 0.4572705108694906 16.36043311774479 chr16 90354753 50992803 0.5643621536987655 15.610136181889127 chr17 81195210 51550316 0.6348935608393648 13.411045930914266 chr18 78077248 44563958 0.5707675301260619 33.111918011666916 chr19 59128983 42930305 0.7260450429191383 25.315570250533714 chr20 63025520 30917543 0.4905559367062739 13.565505845665063 chr21 48129895 5881245 0.12219525930817011 4.882749712606673 chr22 51304566 11162486 0.21757295442280908 5.167173589451154 chrMT 16571 2389 0.1441675215738338 0.5606417927510746 chrX 155270560 81623687 0.5256868204764638 16.277120114134682 chrY 59373566 6720584 0.1131915169117516 4.015180245193545