BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514753.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 79,277,973 number of mapped reads = 75,125,323 (94.76%) number of supplementary alignments = 10,535,786 (13.29%) number of secondary alignments = 0 number of mapped bases = 7,172,218,284 bp number of sequenced bases = 7,167,603,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,480,487 duplication rate = 47.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4935 >>>>>>> ACTG content number of A's = 2,232,441,410 bp (31.15%) number of C's = 1,344,308,133 bp (18.76%) number of T's = 2,201,642,000 bp (30.72%) number of G's = 1,388,718,824 bp (19.37%) number of N's = 492,682 bp (0.01%) GC percentage = 38.13% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 37,984,791 number of insertions = 4,708,125 mapped reads with insertion percentage = 6.01% number of deletions = 1,699,682 mapped reads with deletion percentage = 2.14% homopolymer indels = 54.3% >>>>>>> Coverage mean coverageData = 2.3168X std coverageData = 76.5188X There is a 6.06% of reference with a coverageData >= 1X There is a 4.15% of reference with a coverageData >= 2X There is a 3.42% of reference with a coverageData >= 3X There is a 3.01% of reference with a coverageData >= 4X There is a 2.73% of reference with a coverageData >= 5X There is a 2.53% of reference with a coverageData >= 6X There is a 2.36% of reference with a coverageData >= 7X There is a 2.23% of reference with a coverageData >= 8X There is a 2.12% of reference with a coverageData >= 9X There is a 2.02% of reference with a coverageData >= 10X There is a 1.93% of reference with a coverageData >= 11X There is a 1.85% of reference with a coverageData >= 12X There is a 1.78% of reference with a coverageData >= 13X There is a 1.72% of reference with a coverageData >= 14X There is a 1.66% of reference with a coverageData >= 15X There is a 1.61% of reference with a coverageData >= 16X There is a 1.56% of reference with a coverageData >= 17X There is a 1.51% of reference with a coverageData >= 18X There is a 1.47% of reference with a coverageData >= 19X There is a 1.43% of reference with a coverageData >= 20X There is a 1.4% of reference with a coverageData >= 21X There is a 1.36% of reference with a coverageData >= 22X There is a 1.33% of reference with a coverageData >= 23X There is a 1.3% of reference with a coverageData >= 24X There is a 1.27% of reference with a coverageData >= 25X There is a 1.24% of reference with a coverageData >= 26X There is a 1.21% of reference with a coverageData >= 27X There is a 1.19% of reference with a coverageData >= 28X There is a 1.16% of reference with a coverageData >= 29X There is a 1.14% of reference with a coverageData >= 30X There is a 1.12% of reference with a coverageData >= 31X There is a 1.1% of reference with a coverageData >= 32X There is a 1.08% of reference with a coverageData >= 33X There is a 1.06% of reference with a coverageData >= 34X There is a 1.04% of reference with a coverageData >= 35X There is a 1.02% of reference with a coverageData >= 36X There is a 1% of reference with a coverageData >= 37X There is a 0.98% of reference with a coverageData >= 38X There is a 0.97% of reference with a coverageData >= 39X There is a 0.95% of reference with a coverageData >= 40X There is a 0.94% of reference with a coverageData >= 41X There is a 0.92% of reference with a coverageData >= 42X There is a 0.91% of reference with a coverageData >= 43X There is a 0.89% of reference with a coverageData >= 44X There is a 0.88% of reference with a coverageData >= 45X There is a 0.87% of reference with a coverageData >= 46X There is a 0.86% of reference with a coverageData >= 47X There is a 0.84% of reference with a coverageData >= 48X There is a 0.83% of reference with a coverageData >= 49X There is a 0.82% of reference with a coverageData >= 50X There is a 0.81% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 487917857 1.9575391830217346 41.06834151182921 chr2 243199373 823826257 3.387452224229213 186.66823243366449 chr3 198022430 509902818 2.5749750571185293 36.59508875614789 chr4 191154276 592968108 3.1020394647096463 41.118459399859674 chr5 180915260 320996630 1.7742927268821878 31.750956660047844 chr6 171115067 383830752 2.243114874273462 35.07394095233258 chr7 159138663 391453242 2.4598248761207704 39.39335557569351 chr8 146364022 373351432 2.5508415722546895 92.33764064915803 chr9 141213431 422924363 2.994930156466491 81.39942798831684 chr10 135534747 280191959 2.067307204992975 48.4535263165898 chr11 135006516 270092658 2.000589793754844 36.10736741171124 chr12 133851895 346831352 2.5911575775598843 39.741593208699165 chr13 115169878 300916520 2.6128057546435883 40.94989006351686 chr14 107349540 267927992 2.4958466706052023 36.4203818116445 chr15 102531392 154844794 1.5102183924314614 25.369054302157295 chr16 90354753 160636959 1.7778473590647743 47.76888938074954 chr17 81195210 98396639 1.2118527558460652 24.132702646628555 chr18 78077248 116803705 1.4960018186091806 32.76934490937296 chr19 59128983 37977165 0.6422766479849653 17.241244489734264 chr20 63025520 176719935 2.8039425140800107 65.92679259748388 chr21 48129895 97056721 2.016557921017696 77.27057030948426 chr22 51304566 75272030 1.467160447278708 91.62137045519164 chrMT 16571 169683850 10239.807495021423 9157.663408184366 chrX 155270560 168409428 1.0846191834434036 21.990451654698205 chrY 59373566 143285118 2.4132813245544322 52.41500692828671