BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124779.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 = 648,198 number of mapped reads = 647,655 (99.92%) number of supplementary alignments = 262,666 (40.52%) number of secondary alignments = 0 number of mapped bases = 96,881,485 bp number of sequenced bases = 96,842,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 907,499 duplication rate = 31.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2181 >>>>>>> ACTG content number of A's = 28,011,230 bp (28.92%) number of C's = 18,014,726 bp (18.6%) number of T's = 31,239,165 bp (32.26%) number of G's = 19,577,302 bp (20.22%) number of N's = 0 bp (0%) GC percentage = 38.82% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 711,455 number of insertions = 26,981 mapped reads with insertion percentage = 4.15% number of deletions = 37,040 mapped reads with deletion percentage = 5.59% homopolymer indels = 81% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 49.9982X There is a 0.01% 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 30611 1.2281213132865173E-4 0.040370164323942165 chr2 243199373 21316 8.76482522839399E-5 0.02168891023887227 chr3 198022430 19160 9.675671589324503E-5 0.023430731098053197 chr4 191154276 12584 6.583164270936843E-5 0.01158363009332389 chr5 180915260 16953 9.370685480041872E-5 0.01020568531779786 chr6 171115067 12070 7.053733029833077E-5 0.015024769737523275 chr7 159138663 19908 1.2509844952008928E-4 0.053259904866365164 chr8 146364022 81486828 0.5567408362145172 220.5860143849012 chr9 141213431 8163 5.780611619018024E-5 0.008199714624046797 chr10 135534747 15165069 0.11189063569063953 67.46165713045299 chr11 135006516 13487 9.98988819176698E-5 0.010318972397272063 chr12 133851895 11399 8.516128964778572E-5 0.015249289287685461 chr13 115169878 7765 6.742214314058751E-5 0.016385536315750283 chr14 107349540 7078 6.59341437327072E-5 0.012101342299700297 chr15 102531392 7726 7.535253203233601E-5 0.008677447540882507 chr16 90354753 4327 4.7889013652663074E-5 0.00691842376862523 chr17 81195210 7017 8.642135416608935E-5 0.018161147087734034 chr18 78077248 4135 5.2960370734378344E-5 0.007274554729874273 chr19 59128983 2160 3.6530308664365156E-5 0.010638372698694666 chr20 63025520 4908 7.787321707143393E-5 0.010437142249842327 chr21 48129895 3442 7.151480384488685E-5 0.01580368619240339 chr22 51304566 1195 2.329227382997451E-5 0.004826150774681033 chrMT 16571 285 0.017198720656568703 0.13001124822239812 chrX 155270560 13594 8.755040234285237E-5 0.016416925112106923 chrY 59373566 305 5.136966171107189E-6 0.0022664818072699695