BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153329.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 111,367,544 number of mapped reads = 109,336,091 (98.18%) number of supplementary alignments = 545,674 (0.49%) number of secondary alignments = 0 number of mapped bases = 10,628,627,825 bp number of sequenced bases = 10,626,911,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,980,295 duplication rate = 32.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.6538 >>>>>>> ACTG content number of A's = 2,742,887,130 bp (25.81%) number of C's = 2,570,234,581 bp (24.19%) number of T's = 2,775,165,189 bp (26.11%) number of G's = 2,535,884,498 bp (23.86%) number of N's = 2,740,526 bp (0.03%) GC percentage = 48.05% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 40,589,299 number of insertions = 593,223 mapped reads with insertion percentage = 0.53% number of deletions = 777,895 mapped reads with deletion percentage = 0.7% homopolymer indels = 44.42% >>>>>>> Coverage mean coverageData = 3.4334X std coverageData = 24.7194X There is a 49.86% of reference with a coverageData >= 1X There is a 32.64% of reference with a coverageData >= 2X There is a 20.43% of reference with a coverageData >= 3X There is a 14.23% of reference with a coverageData >= 4X There is a 10.19% of reference with a coverageData >= 5X There is a 7.88% of reference with a coverageData >= 6X There is a 6.39% of reference with a coverageData >= 7X There is a 5.44% of reference with a coverageData >= 8X There is a 4.79% of reference with a coverageData >= 9X There is a 4.33% of reference with a coverageData >= 10X There is a 3.99% of reference with a coverageData >= 11X There is a 3.73% of reference with a coverageData >= 12X There is a 3.51% of reference with a coverageData >= 13X There is a 3.34% of reference with a coverageData >= 14X There is a 3.18% of reference with a coverageData >= 15X There is a 3.05% of reference with a coverageData >= 16X There is a 2.93% of reference with a coverageData >= 17X There is a 2.82% of reference with a coverageData >= 18X There is a 2.72% of reference with a coverageData >= 19X There is a 2.63% of reference with a coverageData >= 20X There is a 2.55% of reference with a coverageData >= 21X There is a 2.47% of reference with a coverageData >= 22X There is a 2.39% of reference with a coverageData >= 23X There is a 2.32% of reference with a coverageData >= 24X There is a 2.26% of reference with a coverageData >= 25X There is a 2.19% of reference with a coverageData >= 26X There is a 2.13% of reference with a coverageData >= 27X There is a 2.08% of reference with a coverageData >= 28X There is a 2.02% of reference with a coverageData >= 29X There is a 1.97% of reference with a coverageData >= 30X There is a 1.92% of reference with a coverageData >= 31X There is a 1.87% of reference with a coverageData >= 32X There is a 1.83% of reference with a coverageData >= 33X There is a 1.78% of reference with a coverageData >= 34X There is a 1.74% of reference with a coverageData >= 35X There is a 1.7% of reference with a coverageData >= 36X There is a 1.66% of reference with a coverageData >= 37X There is a 1.62% of reference with a coverageData >= 38X There is a 1.58% of reference with a coverageData >= 39X There is a 1.55% of reference with a coverageData >= 40X There is a 1.51% of reference with a coverageData >= 41X There is a 1.48% of reference with a coverageData >= 42X There is a 1.45% of reference with a coverageData >= 43X There is a 1.42% of reference with a coverageData >= 44X There is a 1.39% of reference with a coverageData >= 45X There is a 1.36% of reference with a coverageData >= 46X There is a 1.33% of reference with a coverageData >= 47X There is a 1.3% of reference with a coverageData >= 48X There is a 1.28% of reference with a coverageData >= 49X There is a 1.25% of reference with a coverageData >= 50X There is a 1.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1010628430 4.054667651159032 24.150867347903922 chr2 243199373 646356339 2.6577220616436374 13.136814191044287 chr3 198022430 524552900 2.6489569893673157 13.20155129914396 chr4 191154276 390906204 2.044977555197353 15.389139942739513 chr5 180915260 759379172 4.19743017808448 56.25596576848006 chr6 171115067 301970500 1.7647218640308278 10.209875037764524 chr7 159138663 545705165 3.429117442063718 23.06395928198447 chr8 146364022 599506018 4.095993057638167 39.19156191976392 chr9 141213431 293217676 2.076414926849274 11.498017752155855 chr10 135534747 520852177 3.8429420390624998 19.52240273701671 chr11 135006516 505708877 3.7458108836761626 17.562262572221375 chr12 133851895 469876381 3.510420087814222 17.26477389167807 chr13 115169878 119374909 1.0365115520917718 6.378629096937754 chr14 107349540 278740334 2.5965675679653586 14.054757637361528 chr15 102531392 559466915 5.456542665489219 28.464739339391663 chr16 90354753 571988862 6.330478951118376 36.91360420077024 chr17 81195210 483070911 5.949500112137157 26.920355203234184 chr18 78077248 119258101 1.5274373015811213 8.065805278181257 chr19 59128983 617505295 10.443360661217529 41.27011384248766 chr20 63025520 299879663 4.758067255930613 22.113911281884043 chr21 48129895 134162166 2.78750173878418 24.736519936766737 chr22 51304566 233111285 4.543675215964209 25.787938008905495 chrMT 16571 21831 1.3174220022931629 1.8167844555054216 chrX 155270560 630736784 4.062178844463497 21.244676367869022 chrY 59373566 12650930 0.2130734407968691 7.600020657912459