BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514718.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 = 60,643,161 number of mapped reads = 57,305,095 (94.5%) number of supplementary alignments = 3,234,895 (5.33%) number of secondary alignments = 0 number of mapped bases = 5,293,355,726 bp number of sequenced bases = 5,287,328,174 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,394,421 duplication rate = 36.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7069 >>>>>>> ACTG content number of A's = 1,404,383,948 bp (26.56%) number of C's = 1,197,966,552 bp (22.66%) number of T's = 1,417,629,071 bp (26.81%) number of G's = 1,203,504,684 bp (22.76%) number of N's = 63,843,919 bp (1.21%) GC percentage = 45.42% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 53,819,326 number of insertions = 2,887,127 mapped reads with insertion percentage = 4.79% number of deletions = 2,250,298 mapped reads with deletion percentage = 3.63% homopolymer indels = 33.48% >>>>>>> Coverage mean coverageData = 1.7099X std coverageData = 125.2974X There is a 9.57% of reference with a coverageData >= 1X There is a 5.06% of reference with a coverageData >= 2X There is a 3.27% of reference with a coverageData >= 3X There is a 2.46% of reference with a coverageData >= 4X There is a 1.99% of reference with a coverageData >= 5X There is a 1.69% of reference with a coverageData >= 6X There is a 1.48% of reference with a coverageData >= 7X There is a 1.33% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 1.11% of reference with a coverageData >= 10X There is a 1.03% of reference with a coverageData >= 11X There is a 0.97% of reference with a coverageData >= 12X There is a 0.92% of reference with a coverageData >= 13X There is a 0.87% of reference with a coverageData >= 14X There is a 0.83% of reference with a coverageData >= 15X There is a 0.79% of reference with a coverageData >= 16X There is a 0.76% of reference with a coverageData >= 17X There is a 0.73% of reference with a coverageData >= 18X There is a 0.7% of reference with a coverageData >= 19X There is a 0.68% of reference with a coverageData >= 20X There is a 0.66% of reference with a coverageData >= 21X There is a 0.64% of reference with a coverageData >= 22X There is a 0.62% of reference with a coverageData >= 23X There is a 0.6% of reference with a coverageData >= 24X There is a 0.58% of reference with a coverageData >= 25X There is a 0.57% of reference with a coverageData >= 26X There is a 0.55% of reference with a coverageData >= 27X There is a 0.54% of reference with a coverageData >= 28X There is a 0.53% of reference with a coverageData >= 29X There is a 0.52% of reference with a coverageData >= 30X There is a 0.5% of reference with a coverageData >= 31X There is a 0.49% of reference with a coverageData >= 32X There is a 0.48% of reference with a coverageData >= 33X There is a 0.47% of reference with a coverageData >= 34X There is a 0.47% of reference with a coverageData >= 35X There is a 0.46% of reference with a coverageData >= 36X There is a 0.45% of reference with a coverageData >= 37X There is a 0.44% of reference with a coverageData >= 38X There is a 0.43% of reference with a coverageData >= 39X There is a 0.43% of reference with a coverageData >= 40X There is a 0.42% of reference with a coverageData >= 41X There is a 0.41% of reference with a coverageData >= 42X There is a 0.41% of reference with a coverageData >= 43X There is a 0.4% of reference with a coverageData >= 44X There is a 0.39% of reference with a coverageData >= 45X There is a 0.39% of reference with a coverageData >= 46X There is a 0.38% of reference with a coverageData >= 47X There is a 0.38% of reference with a coverageData >= 48X There is a 0.37% of reference with a coverageData >= 49X There is a 0.37% of reference with a coverageData >= 50X There is a 0.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 462010144 1.8535967619514977 210.53869610010727 chr2 243199373 400181467 1.6454872480283902 70.98761528755827 chr3 198022430 297310315 1.5013971649575253 32.750046968487524 chr4 191154276 251985651 1.3182318296662117 49.61456493311402 chr5 180915260 277913587 1.5361533736844533 67.70571716201748 chr6 171115067 216725302 1.2665471591698 51.79534254300859 chr7 159138663 260386841 1.636226144491361 40.91489810387969 chr8 146364022 209066122 1.428398312257366 46.300304987207554 chr9 141213431 252236515 1.786207680202884 87.62776433589598 chr10 135534747 349859052 2.581323680782759 126.1575291948393 chr11 135006516 353050121 2.6150598612588447 146.76875249336945 chr12 133851895 270545484 2.021230136487795 47.63499504558984 chr13 115169878 97617517 0.8475959052418203 35.19915628345507 chr14 107349540 103160336 0.9609760414436801 23.17319267010968 chr15 102531392 233497545 2.2773273672125702 274.9734476510558 chr16 90354753 202085360 2.236576973432709 74.55828606078471 chr17 81195210 172372119 2.12293457951522 41.587690311469835 chr18 78077248 190962165 2.445810654084529 67.83651195259002 chr19 59128983 117010274 1.9788988083897874 45.91712818108479 chr20 63025520 109989313 1.745155184756905 61.53136394724459 chr21 48129895 219019896 4.550599913006251 603.7048140402401 chr22 51304566 47017757 0.9164439087156492 23.441834906261676 chrMT 16571 2418620 145.95498159435158 212.71780180743377 chrX 155270560 156597363 1.0085451034632709 49.85457892201629 chrY 59373566 40336860 0.679374050061268 27.83811523041479