BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514722.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 = 167,397,893 number of mapped reads = 152,994,499 (91.4%) number of supplementary alignments = 10,685,630 (6.38%) number of secondary alignments = 0 number of mapped bases = 13,796,590,267 bp number of sequenced bases = 13,770,128,772 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,674,811 duplication rate = 49.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.462 >>>>>>> ACTG content number of A's = 3,649,136,405 bp (26.5%) number of C's = 3,116,711,975 bp (22.63%) number of T's = 3,679,462,735 bp (26.72%) number of G's = 3,156,764,176 bp (22.92%) number of N's = 168,053,481 bp (1.22%) GC percentage = 45.56% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 165,364,243 number of insertions = 10,458,825 mapped reads with insertion percentage = 6.32% number of deletions = 7,940,310 mapped reads with deletion percentage = 4.74% homopolymer indels = 31.05% >>>>>>> Coverage mean coverageData = 4.4567X std coverageData = 389.1126X There is a 7.19% of reference with a coverageData >= 1X There is a 3.92% of reference with a coverageData >= 2X There is a 2.58% of reference with a coverageData >= 3X There is a 1.98% of reference with a coverageData >= 4X There is a 1.63% of reference with a coverageData >= 5X There is a 1.41% of reference with a coverageData >= 6X There is a 1.26% of reference with a coverageData >= 7X There is a 1.14% of reference with a coverageData >= 8X There is a 1.06% of reference with a coverageData >= 9X There is a 0.99% of reference with a coverageData >= 10X There is a 0.94% of reference with a coverageData >= 11X There is a 0.89% of reference with a coverageData >= 12X There is a 0.85% of reference with a coverageData >= 13X There is a 0.82% of reference with a coverageData >= 14X There is a 0.79% of reference with a coverageData >= 15X There is a 0.77% of reference with a coverageData >= 16X There is a 0.74% of reference with a coverageData >= 17X There is a 0.72% of reference with a coverageData >= 18X There is a 0.71% of reference with a coverageData >= 19X There is a 0.69% of reference with a coverageData >= 20X There is a 0.67% of reference with a coverageData >= 21X There is a 0.66% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.63% of reference with a coverageData >= 24X There is a 0.62% of reference with a coverageData >= 25X There is a 0.61% of reference with a coverageData >= 26X There is a 0.6% of reference with a coverageData >= 27X There is a 0.59% of reference with a coverageData >= 28X There is a 0.58% of reference with a coverageData >= 29X There is a 0.57% of reference with a coverageData >= 30X There is a 0.57% of reference with a coverageData >= 31X There is a 0.56% of reference with a coverageData >= 32X There is a 0.55% of reference with a coverageData >= 33X There is a 0.54% of reference with a coverageData >= 34X There is a 0.54% of reference with a coverageData >= 35X There is a 0.53% of reference with a coverageData >= 36X There is a 0.52% of reference with a coverageData >= 37X There is a 0.52% of reference with a coverageData >= 38X There is a 0.51% of reference with a coverageData >= 39X There is a 0.51% of reference with a coverageData >= 40X There is a 0.5% of reference with a coverageData >= 41X There is a 0.5% of reference with a coverageData >= 42X There is a 0.49% 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 0.47% of reference with a coverageData >= 48X There is a 0.46% of reference with a coverageData >= 49X There is a 0.46% of reference with a coverageData >= 50X There is a 0.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1023099449 4.104701705036073 151.75191344124434 chr2 243199373 1403939110 5.77279082870004 733.7068665645062 chr3 198022430 641801090 3.2410524908718674 103.42724404742445 chr4 191154276 752718378 3.9377532836356743 247.90308329875975 chr5 180915260 808257949 4.4676051594542106 302.5351250027179 chr6 171115067 592170645 3.4606575293571313 212.69335055993082 chr7 159138663 460259380 2.8921908185190675 140.04095977642052 chr8 146364022 510813751 3.4900226436794695 176.45030527397972 chr9 141213431 731909885 5.1830047596534925 251.73189155645278 chr10 135534747 830168309 6.125132686454197 373.0940248336798 chr11 135006516 728907436 5.399053746413247 188.2377230016153 chr12 133851895 566020165 4.22870490552263 201.9141715676527 chr13 115169878 768201723 6.670161819568828 1043.6394484745988 chr14 107349540 450434121 4.195957625901332 252.26129807913628 chr15 102531392 278980644 2.7209290594630766 105.37632667279044 chr16 90354753 662094156 7.327718067028527 502.6925166653752 chr17 81195210 306042648 3.7692204749516627 148.30003190057263 chr18 78077248 311806567 3.9935650267796325 153.59050384284927 chr19 59128983 457942490 7.744805791772201 523.8510810656583 chr20 63025520 223194318 3.541332431687989 222.0515558072485 chr21 48129895 345404592 7.17650832190679 741.2324398892204 chr22 51304566 290034093 5.653182857057986 573.1017537802351 chrMT 16571 3231196 194.99100838814797 267.7249960750892 chrX 155270560 397130199 2.5576657867402552 149.64509246372384 chrY 59373566 252027973 4.244784168766282 611.0837045251119