BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328246.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 603,411,566 number of mapped reads = 590,043,456 (97.78%) number of supplementary alignments = 31,178,808 (5.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 297,072,535 number of mapped paired reads (second in pair) = 292,970,921 number of mapped paired reads (both in pair) = 582,393,082 number of mapped paired reads (singletons) = 7,650,374 number of mapped bases = 81,879,569,934 bp number of sequenced bases = 81,686,992,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 340,823,639 duplication rate = 45.94% >>>>>>> Insert size mean insert size = 412,613.2949 std insert size = 6,656,853.613 median insert size = 375 >>>>>>> Mapping quality mean mapping quality = 52.9244 >>>>>>> ACTG content number of A's = 23,032,286,543 bp (28.2%) number of C's = 17,259,661,795 bp (21.13%) number of T's = 22,865,434,139 bp (27.99%) number of G's = 18,528,141,481 bp (22.68%) number of N's = 1,468,967 bp (0%) GC percentage = 43.81% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 967,145,563 number of insertions = 20,708,719 mapped reads with insertion percentage = 3.18% number of deletions = 66,421,809 mapped reads with deletion percentage = 10.57% homopolymer indels = 47.65% >>>>>>> Coverage mean coverageData = 26.4495X std coverageData = 1,002.5069X There is a 92.11% of reference with a coverageData >= 1X There is a 91.74% of reference with a coverageData >= 2X There is a 91.2% of reference with a coverageData >= 3X There is a 90.44% of reference with a coverageData >= 4X There is a 89.42% of reference with a coverageData >= 5X There is a 88.1% of reference with a coverageData >= 6X There is a 86.47% of reference with a coverageData >= 7X There is a 84.53% of reference with a coverageData >= 8X There is a 82.28% of reference with a coverageData >= 9X There is a 79.77% of reference with a coverageData >= 10X There is a 77.02% of reference with a coverageData >= 11X There is a 74.08% of reference with a coverageData >= 12X There is a 71% of reference with a coverageData >= 13X There is a 67.83% of reference with a coverageData >= 14X There is a 64.61% of reference with a coverageData >= 15X There is a 61.38% of reference with a coverageData >= 16X There is a 58.19% of reference with a coverageData >= 17X There is a 55.05% of reference with a coverageData >= 18X There is a 52% of reference with a coverageData >= 19X There is a 49.06% of reference with a coverageData >= 20X There is a 46.23% of reference with a coverageData >= 21X There is a 43.54% of reference with a coverageData >= 22X There is a 40.98% of reference with a coverageData >= 23X There is a 38.56% of reference with a coverageData >= 24X There is a 36.27% of reference with a coverageData >= 25X There is a 34.12% of reference with a coverageData >= 26X There is a 32.11% of reference with a coverageData >= 27X There is a 30.22% of reference with a coverageData >= 28X There is a 28.46% of reference with a coverageData >= 29X There is a 26.81% of reference with a coverageData >= 30X There is a 25.27% of reference with a coverageData >= 31X There is a 23.83% of reference with a coverageData >= 32X There is a 22.49% of reference with a coverageData >= 33X There is a 21.24% of reference with a coverageData >= 34X There is a 20.07% of reference with a coverageData >= 35X There is a 18.99% of reference with a coverageData >= 36X There is a 17.97% of reference with a coverageData >= 37X There is a 17.02% of reference with a coverageData >= 38X There is a 16.14% of reference with a coverageData >= 39X There is a 15.31% of reference with a coverageData >= 40X There is a 14.54% of reference with a coverageData >= 41X There is a 13.81% of reference with a coverageData >= 42X There is a 13.13% of reference with a coverageData >= 43X There is a 12.5% of reference with a coverageData >= 44X There is a 11.9% of reference with a coverageData >= 45X There is a 11.34% of reference with a coverageData >= 46X There is a 10.81% of reference with a coverageData >= 47X There is a 10.32% of reference with a coverageData >= 48X There is a 9.85% of reference with a coverageData >= 49X There is a 9.41% of reference with a coverageData >= 50X There is a 9% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6564524350 26.337043108109246 398.45976915032276 chr2 243199373 7526810694 30.949136920677834 3443.5592555971148 chr3 198022430 5059037451 25.547800069921372 35.97773830427221 chr4 191154276 5220905272 27.312521494418466 481.87942460494787 chr5 180915260 4573996165 25.282533739829354 39.2389832691547 chr6 171115067 4374861470 25.566781153175718 75.62839534056798 chr7 159138663 4302694177 27.03739051144347 160.9813925590299 chr8 146364022 4837318353 33.04991409022635 407.0386760774285 chr9 141213431 3388736583 23.997268241432362 254.29332380564938 chr10 135534747 4525907319 33.39296688988544 525.4775379843435 chr11 135006516 3576682441 26.492665294762514 86.1198510439602 chr12 133851895 3604062578 26.925749373962915 100.91406529679509 chr13 115169878 2349631141 20.40143813471783 52.993732063807656 chr14 107349540 2404386403 22.397733637237756 55.26604919750739 chr15 102531392 2286758168 22.303005190839503 30.998819254613952 chr16 90354753 2863171494 31.68811157062208 258.1731285512284 chr17 81195210 3048818110 37.54923609409964 128.6159489533429 chr18 78077248 2032209161 26.028186354621514 212.67396390231434 chr19 59128983 2029332823 34.3204418550544 305.80699092202525 chr20 63025520 1756084417 27.863069071068356 134.575768057571 chr21 48129895 1151475780 23.924336007797233 232.26258454508036 chr22 51304566 1108948949 21.615014714284886 44.87480754589585 chrMT 16571 629957621 38015.6671896687 20827.50309470803 chrX 155270560 2111244359 13.597196783472668 37.945413087123235 chrY 59373566 552014655 9.297313471116086 452.90277020812624