BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472422.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 = 18,636,010 number of mapped reads = 18,370,128 (98.57%) number of supplementary alignments = 28,260 (0.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,256,838 number of mapped paired reads (second in pair) = 9,113,290 number of mapped paired reads (both in pair) = 18,184,278 number of mapped paired reads (singletons) = 185,850 number of mapped bases = 1,806,554,936 bp number of sequenced bases = 1,806,305,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,836,695 duplication rate = 44.87% >>>>>>> Insert size mean insert size = 36,689.3374 std insert size = 1,912,259.0719 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 54.9113 >>>>>>> ACTG content number of A's = 513,802,810 bp (28.44%) number of C's = 390,601,236 bp (21.62%) number of T's = 514,967,536 bp (28.51%) number of G's = 386,695,954 bp (21.41%) number of N's = 238,462 bp (0.01%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 10,128,737 number of insertions = 85,479 mapped reads with insertion percentage = 0.46% number of deletions = 107,331 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.44% >>>>>>> Coverage mean coverageData = 0.5836X std coverageData = 11.4594X There is a 5.35% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.65% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.54% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.51% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.49% of reference with a coverageData >= 13X There is a 0.48% of reference with a coverageData >= 14X There is a 0.46% of reference with a coverageData >= 15X There is a 0.45% of reference with a coverageData >= 16X There is a 0.45% of reference with a coverageData >= 17X There is a 0.44% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.42% of reference with a coverageData >= 20X There is a 0.41% of reference with a coverageData >= 21X There is a 0.4% of reference with a coverageData >= 22X There is a 0.4% of reference with a coverageData >= 23X There is a 0.39% of reference with a coverageData >= 24X There is a 0.38% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.37% of reference with a coverageData >= 27X There is a 0.37% of reference with a coverageData >= 28X There is a 0.36% of reference with a coverageData >= 29X There is a 0.36% of reference with a coverageData >= 30X There is a 0.35% of reference with a coverageData >= 31X There is a 0.34% of reference with a coverageData >= 32X There is a 0.34% of reference with a coverageData >= 33X There is a 0.33% of reference with a coverageData >= 34X There is a 0.33% of reference with a coverageData >= 35X There is a 0.33% of reference with a coverageData >= 36X There is a 0.32% of reference with a coverageData >= 37X There is a 0.32% of reference with a coverageData >= 38X There is a 0.31% of reference with a coverageData >= 39X There is a 0.31% of reference with a coverageData >= 40X There is a 0.3% of reference with a coverageData >= 41X There is a 0.3% of reference with a coverageData >= 42X There is a 0.3% of reference with a coverageData >= 43X There is a 0.29% of reference with a coverageData >= 44X There is a 0.29% of reference with a coverageData >= 45X There is a 0.28% of reference with a coverageData >= 46X There is a 0.28% of reference with a coverageData >= 47X There is a 0.28% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.27% of reference with a coverageData >= 50X There is a 0.27% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 202070670 0.8107128046032029 14.32880388487948 chr2 243199373 138771008 0.5706059447776619 12.183372898584244 chr3 198022430 165178611 0.8341409152488433 12.84718435681384 chr4 191154276 70057289 0.36649605996781365 9.32219457106682 chr5 180915260 90602071 0.5007983903624271 10.384682879618637 chr6 171115067 133382055 0.779487495393962 12.496717254061252 chr7 159138663 109749682 0.6896481340929702 14.093617468546224 chr8 146364022 110769478 0.7568081041118151 13.520115573536133 chr9 141213431 88803596 0.6288608340661307 10.507505821717944 chr10 135534747 47994525 0.3541123295858589 8.128864130490525 chr11 135006516 70211755 0.5200619724162054 11.134409135893689 chr12 133851895 76843666 0.5740947186440655 9.448610065324878 chr13 115169878 49992935 0.4340799510094124 11.130513139712521 chr14 107349540 48382408 0.45069972353863835 9.296413139507782 chr15 102531392 42919706 0.4186006369639456 9.964104107713597 chr16 90354753 82603665 0.914214938975042 16.872819087989125 chr17 81195210 82879548 1.0207443025272058 15.566448679393597 chr18 78077248 30644501 0.39248951243773345 7.929265940350291 chr19 59128983 34934892 0.5908251795908616 8.089903674928346 chr20 63025520 32709876 0.5189941471327805 9.814105018819086 chr21 48129895 15694069 0.3260773579497732 13.076603900109562 chr22 51304566 24974923 0.48679727648412424 10.085331348347585 chrMT 16571 1513593 91.3398708587291 19.879388379132138 chrX 155270560 51532589 0.33188898784161014 5.2363824706203275 chrY 59373566 3337825 0.05621735773795362 1.7083466786589103