BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080970.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,840,001 number of mapped reads = 6,089,285 (89.02%) number of supplementary alignments = 70,676 (1.03%) number of secondary alignments = 0 number of mapped bases = 411,610,701 bp number of sequenced bases = 411,457,808 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 465,397 duplication rate = 5.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.843 >>>>>>> ACTG content number of A's = 116,468,273 bp (28.31%) number of C's = 73,744,662 bp (17.92%) number of T's = 132,457,695 bp (32.19%) number of G's = 87,962,618 bp (21.38%) number of N's = 824,560 bp (0.2%) GC percentage = 39.3% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 4,155,123 number of insertions = 33,186 mapped reads with insertion percentage = 0.54% number of deletions = 92,527 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.74% >>>>>>> Coverage mean coverageData = 0.133X std coverageData = 0.9208X There is a 8.63% of reference with a coverageData >= 1X There is a 2.79% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 33945752 0.13619124343124506 1.3194648049939044 chr2 243199373 27795100 0.1142893571522489 0.8543795815250387 chr3 198022430 36156403 0.18258741194116243 0.6077753808599181 chr4 191154276 26390225 0.13805720464239052 0.5830785347032572 chr5 180915260 24271659 0.1341603743100499 0.5180154895285867 chr6 171115067 35604367 0.20807265908384326 1.03161862085945 chr7 159138663 20476805 0.1286727223540894 1.0800633948912504 chr8 146364022 31606725 0.21594599935221787 1.96549944148676 chr9 141213431 18206671 0.12893016529001408 0.9915730292124816 chr10 135534747 18697549 0.1379539152421187 0.7512210824540347 chr11 135006516 18073995 0.13387498274527726 0.7664335576416631 chr12 133851895 20653197 0.15429887638124212 0.5841068481723207 chr13 115169878 10929129 0.09489572438376638 0.43424075588113337 chr14 107349540 11836643 0.11026263363587771 0.643453759859986 chr15 102531392 10369167 0.10113163195911745 0.44888604786906167 chr16 90354753 9291311 0.10283145813037639 0.5903754880199368 chr17 81195210 8265773 0.10180123926029627 0.4989706682515664 chr18 78077248 10276716 0.13162241579006473 1.7823401016565572 chr19 59128983 7320718 0.1238093000855435 1.0420526819807567 chr20 63025520 6621121 0.10505460327816414 0.5015750366635026 chr21 48129895 8084204 0.1679663751603863 0.7212168043436572 chr22 51304566 3297986 0.06428250460202704 0.35100190784188773 chrMT 16571 343787 20.746303783718545 10.86488319516151 chrX 155270560 12097267 0.07791088664844127 0.47431972111710236 chrY 59373566 998431 0.016816086135031875 0.3320376622314195