BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472404.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 = 20,766,244 number of mapped reads = 20,577,120 (99.09%) number of supplementary alignments = 79,108 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,321,730 number of mapped paired reads (second in pair) = 10,255,390 number of mapped paired reads (both in pair) = 20,460,926 number of mapped paired reads (singletons) = 116,194 number of mapped bases = 2,020,494,690 bp number of sequenced bases = 2,020,255,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,071,314 duplication rate = 47.78% >>>>>>> Insert size mean insert size = 20,342.6102 std insert size = 1,382,584.5558 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 55.0375 >>>>>>> ACTG content number of A's = 547,611,420 bp (27.11%) number of C's = 463,791,579 bp (22.96%) number of T's = 548,187,482 bp (27.13%) number of G's = 460,410,496 bp (22.79%) number of N's = 254,927 bp (0.01%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 11,413,253 number of insertions = 114,207 mapped reads with insertion percentage = 0.55% number of deletions = 99,724 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.6527X std coverageData = 19.1702X There is a 5.74% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.33% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 254196667 1.0198436657054508 27.454303762879448 chr2 243199373 143125833 0.5885123437386494 16.88274145712783 chr3 198022430 223937395 1.1308688364242374 26.353015661848005 chr4 191154276 72997285 0.38187628614700725 15.780531896199482 chr5 180915260 97543928 0.5391691557693917 15.111707140429875 chr6 171115067 131677937 0.76952859446328 16.928831627721078 chr7 159138663 112430590 0.7064944990771979 21.16746223485376 chr8 146364022 89373495 0.6106247544905536 14.642955629855694 chr9 141213431 97335318 0.689278047496771 17.49109427214123 chr10 135534747 50824209 0.3749902524996044 11.235479043686023 chr11 135006516 89196591 0.6606835998938007 18.79139182272595 chr12 133851895 80269843 0.5996914948421164 17.58133584276536 chr13 115169878 45126653 0.391826871606133 13.880828776454862 chr14 107349540 49400795 0.4601863687538857 13.32132738113938 chr15 102531392 56717273 0.5531698330985304 21.393992296100627 chr16 90354753 83003134 0.918636056699751 23.89394635757588 chr17 81195210 76323849 0.9400043303047064 21.558117882753926 chr18 78077248 49985214 0.6402020470803479 25.551933052204372 chr19 59128983 49943162 0.8446477423770337 18.761665493534764 chr20 63025520 51928892 0.8239343681734003 25.06652688959978 chr21 48129895 13188401 0.27401682467830024 17.023589516647043 chr22 51304566 25407956 0.49523771431961827 15.04920771647517 chrMT 16571 29769 1.7964516323698028 1.8212961299574861 chrX 155270560 73698142 0.4746433709004463 15.624501397286107 chrY 59373566 2832359 0.04770404054895406 2.651574019542602