BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124807.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 686,414 number of mapped reads = 685,609 (99.88%) number of supplementary alignments = 314,847 (45.87%) number of secondary alignments = 0 number of mapped bases = 103,339,602 bp number of sequenced bases = 103,296,067 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 999,039 duplication rate = 34.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.7457 >>>>>>> ACTG content number of A's = 27,861,919 bp (26.97%) number of C's = 19,797,448 bp (19.17%) number of T's = 33,421,180 bp (32.35%) number of G's = 22,215,519 bp (21.51%) number of N's = 1 bp (0%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 733,870 number of insertions = 13,491 mapped reads with insertion percentage = 1.95% number of deletions = 41,097 mapped reads with deletion percentage = 5.85% homopolymer indels = 84.4% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 68.3193X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 61758 2.4777470865358447E-4 0.19042588791729015 chr2 243199373 7757 3.1895641441476905E-5 0.006200719604878068 chr3 198022430 6008 3.0339997342725268E-5 0.005500293917231885 chr4 191154276 4961 2.5952859145039476E-5 0.0053965176279390835 chr5 180915260 4209 2.3265035796317016E-5 0.00874702336640048 chr6 171115067 5611 3.279080035658111E-5 0.009733259767473615 chr7 159138663 6030 3.789148335373409E-5 0.014071541191508453 chr8 146364022 93213852 0.6368631493332426 311.02931108107543 chr9 141213431 3082 2.1825119453403835E-5 0.004670169245007985 chr10 135534747 9987477 0.07368942076528906 46.25939706861255 chr11 135006516 3627 2.6865369964809698E-5 0.005269564337186695 chr12 133851895 4035 3.01452586831139E-5 0.0060977028471408245 chr13 115169878 2389 2.074327108343381E-5 0.0074445985424783844 chr14 107349540 1906 1.7755083067892048E-5 0.00504841760303723 chr15 102531392 2977 2.903501007769406E-5 0.0056291220788172265 chr16 90354753 2827 3.128778405271054E-5 0.005843134143460293 chr17 81195210 2244 2.7637098296808396E-5 0.005254683991849835 chr18 78077248 2061 2.6396934482116992E-5 0.005137726898538588 chr19 59128983 7511 1.2702738350835494E-4 0.05121700270571584 chr20 63025520 1894 3.0051318894314557E-5 0.005481825956061289 chr21 48129895 1045 2.1712077285853212E-5 0.004657341480537034 chr22 51304566 1385 2.699564791172778E-5 0.005729124158364334 chrMT 16571 0 0.0 0.0 chrX 155270560 3908 2.5168969571565918E-5 0.006160035170745698 chrY 59373566 1048 1.765095261416503E-5 0.00419725591584663