BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975234.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 33,656,898 number of mapped reads = 33,574,269 (99.75%) number of supplementary alignments = 169,493 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,787,496 number of mapped paired reads (second in pair) = 16,786,773 number of mapped paired reads (both in pair) = 33,515,138 number of mapped paired reads (singletons) = 59,131 number of mapped bases = 3,171,226,103 bp number of sequenced bases = 3,169,897,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,682,716 duplication rate = 42.61% >>>>>>> Insert size mean insert size = 205,590.9807 std insert size = 4,425,240.5871 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.8951 >>>>>>> ACTG content number of A's = 824,972,062 bp (26.03%) number of C's = 723,183,031 bp (22.81%) number of T's = 858,415,283 bp (27.08%) number of G's = 763,238,906 bp (24.08%) number of N's = 88,477 bp (0%) GC percentage = 46.89% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 23,644,472 number of insertions = 365,959 mapped reads with insertion percentage = 1.08% number of deletions = 896,985 mapped reads with deletion percentage = 2.62% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 1.0244X std coverageData = 16.9499X There is a 7.92% of reference with a coverageData >= 1X There is a 3.87% of reference with a coverageData >= 2X There is a 2.47% of reference with a coverageData >= 3X There is a 1.96% of reference with a coverageData >= 4X There is a 1.7% of reference with a coverageData >= 5X There is a 1.54% of reference with a coverageData >= 6X There is a 1.43% of reference with a coverageData >= 7X There is a 1.34% of reference with a coverageData >= 8X There is a 1.27% of reference with a coverageData >= 9X There is a 1.21% of reference with a coverageData >= 10X There is a 1.16% of reference with a coverageData >= 11X There is a 1.11% of reference with a coverageData >= 12X There is a 1.07% of reference with a coverageData >= 13X There is a 1.03% of reference with a coverageData >= 14X There is a 0.99% of reference with a coverageData >= 15X There is a 0.96% of reference with a coverageData >= 16X There is a 0.93% of reference with a coverageData >= 17X There is a 0.9% of reference with a coverageData >= 18X There is a 0.87% of reference with a coverageData >= 19X There is a 0.84% of reference with a coverageData >= 20X There is a 0.82% of reference with a coverageData >= 21X There is a 0.8% of reference with a coverageData >= 22X There is a 0.78% of reference with a coverageData >= 23X There is a 0.76% of reference with a coverageData >= 24X There is a 0.74% of reference with a coverageData >= 25X There is a 0.72% of reference with a coverageData >= 26X There is a 0.7% of reference with a coverageData >= 27X There is a 0.68% of reference with a coverageData >= 28X There is a 0.67% of reference with a coverageData >= 29X There is a 0.65% of reference with a coverageData >= 30X There is a 0.64% of reference with a coverageData >= 31X There is a 0.62% of reference with a coverageData >= 32X There is a 0.61% of reference with a coverageData >= 33X There is a 0.6% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.57% of reference with a coverageData >= 36X There is a 0.56% of reference with a coverageData >= 37X There is a 0.55% of reference with a coverageData >= 38X There is a 0.54% of reference with a coverageData >= 39X There is a 0.53% of reference with a coverageData >= 40X There is a 0.52% of reference with a coverageData >= 41X There is a 0.51% of reference with a coverageData >= 42X There is a 0.5% of reference with a coverageData >= 43X There is a 0.49% of reference with a coverageData >= 44X There is a 0.48% of reference with a coverageData >= 45X There is a 0.48% of reference with a coverageData >= 46X There is a 0.47% of reference with a coverageData >= 47X There is a 0.46% of reference with a coverageData >= 48X There is a 0.45% of reference with a coverageData >= 49X There is a 0.44% of reference with a coverageData >= 50X There is a 0.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 269166478 1.0799029383361094 15.618610941005791 chr2 243199373 267818571 1.1012305159191345 16.805088552131313 chr3 198022430 173866510 0.8780142229342404 14.52459240328794 chr4 191154276 98398744 0.5147608835075183 9.584636645134044 chr5 180915260 142432077 0.7872861415891617 13.871796731693903 chr6 171115067 159872684 0.9342992806121508 16.00968297164147 chr7 159138663 139518141 0.8767080128101868 14.856936558275127 chr8 146364022 127114620 0.8684826931033639 14.547842099931865 chr9 141213431 126153505 0.893353444545937 13.411177105887782 chr10 135534747 129799865 0.9576869981540601 15.291609787943564 chr11 135006516 242625443 1.7971387618061339 23.806337279426888 chr12 133851895 226369706 1.691195376800605 23.82466157155938 chr13 115169878 49389691 0.4288420883800884 8.405526244867325 chr14 107349540 112458234 1.047589342255216 16.13084055374287 chr15 102531392 79160080 0.7720570105982761 11.559210673939738 chr16 90354753 81763920 0.9049210726081006 14.111843353669464 chr17 81195210 170810484 2.103701486824161 27.317364947503062 chr18 78077248 52303772 0.6698977402482219 12.571753972177 chr19 59128983 153974987 2.6040526859729685 33.76635002292466 chr20 63025520 214288128 3.400021578560558 40.84002378009546 chr21 48129895 22601984 0.46960385016422745 8.882368057511531 chr22 51304566 50884578 0.9918138280323822 14.961090628461713 chrMT 16571 180857 10.914066743105424 15.730286495454862 chrX 155270560 71679880 0.4616450149983358 9.972944162016367 chrY 59373566 8593164 0.14473046810090537 4.6133092551678905