BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472681.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 = 20,102,782 number of mapped reads = 19,936,254 (99.17%) number of supplementary alignments = 119,384 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,994,043 number of mapped paired reads (second in pair) = 9,942,211 number of mapped paired reads (both in pair) = 19,819,878 number of mapped paired reads (singletons) = 116,376 number of mapped bases = 1,962,529,694 bp number of sequenced bases = 1,962,303,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,088,922 duplication rate = 50.75% >>>>>>> Insert size mean insert size = 24,469.9371 std insert size = 1,533,511.5232 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 54.9643 >>>>>>> ACTG content number of A's = 535,443,688 bp (27.29%) number of C's = 449,759,757 bp (22.92%) number of T's = 534,141,548 bp (27.22%) number of G's = 442,583,105 bp (22.55%) number of N's = 375,317 bp (0.02%) GC percentage = 45.47% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 12,591,651 number of insertions = 131,182 mapped reads with insertion percentage = 0.65% number of deletions = 92,239 mapped reads with deletion percentage = 0.46% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.634X std coverageData = 33.7507X There is a 3.77% of reference with a coverageData >= 1X There is a 1.73% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.64% 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 0.41% 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 0.34% 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 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 211198401 0.847333499722755 28.64474411841966 chr2 243199373 156849886 0.6449436282058177 27.060119367322404 chr3 198022430 210601250 1.0635221979651497 37.475175053262085 chr4 191154276 53133807 0.27796295281409245 16.4351292009283 chr5 180915260 55385252 0.30613919467047723 12.734084598720473 chr6 171115067 121541036 0.7102883348080622 22.467048767533527 chr7 159138663 119719738 0.7522982519967508 25.069867540116775 chr8 146364022 102282051 0.6988196252218322 28.02460929611402 chr9 141213431 147128398 1.0418867168520252 27.952879150954274 chr10 135534747 34649304 0.25564886323947617 13.23538720000462 chr11 135006516 34497690 0.25552611105081774 9.87917875562664 chr12 133851895 69810124 0.5215475208625174 15.705765176669734 chr13 115169878 51941969 0.451003073911392 24.354466791145512 chr14 107349540 78577295 0.731976075537911 124.157044147555 chr15 102531392 24446961 0.23843391300100558 13.092979848099214 chr16 90354753 100095550 1.1078061383223525 36.113128810251624 chr17 81195210 74889477 0.9223386083982048 30.447191218000437 chr18 78077248 18088186 0.23167038366926046 12.747365945750644 chr19 59128983 43877011 0.742055905138771 20.946137417510997 chr20 63025520 69911554 1.1092578688759729 28.09477474360555 chr21 48129895 10010595 0.20799120795921122 9.416203790806321 chr22 51304566 29630197 0.5775352821423341 28.253887605641257 chrMT 16571 9158 0.5526522237644077 0.9196464412611678 chrX 155270560 142885783 0.9202374423071573 38.92065103613764 chrY 59373566 1369021 0.023057752670607657 1.6914094953898156