BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975332.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,300,008 number of mapped reads = 4,248,938 (98.81%) number of supplementary alignments = 27,654 (0.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,124,044 number of mapped paired reads (second in pair) = 2,124,894 number of mapped paired reads (both in pair) = 4,238,504 number of mapped paired reads (singletons) = 10,434 number of mapped bases = 413,219,991 bp number of sequenced bases = 413,088,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,013 duplication rate = 1.84% >>>>>>> Insert size mean insert size = 87,194.2474 std insert size = 2,792,044.68 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 53.4577 >>>>>>> ACTG content number of A's = 121,206,831 bp (29.34%) number of C's = 84,340,557 bp (20.42%) number of T's = 123,160,609 bp (29.81%) number of G's = 84,371,788 bp (20.42%) number of N's = 8,363 bp (0%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 2,022,139 number of insertions = 59,355 mapped reads with insertion percentage = 1.36% number of deletions = 54,496 mapped reads with deletion percentage = 1.25% homopolymer indels = 37.9% >>>>>>> Coverage mean coverageData = 0.1335X std coverageData = 1.5097X There is a 10.01% of reference with a coverageData >= 1X There is a 2.43% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 33360904 0.1338448179834224 3.0268905636774432 chr2 243199373 35793329 0.14717689671017367 1.0493003093342268 chr3 198022430 27794515 0.14036043795644765 0.4946918109582936 chr4 191154276 29073999 0.15209703705503297 1.3304973062363405 chr5 180915260 25477808 0.14082730224083917 0.44581080780935783 chr6 171115067 24430830 0.1427742771476693 0.8220314876217447 chr7 159138663 22757817 0.14300620962235933 1.322853663453156 chr8 146364022 21136745 0.14441216298360535 1.7542164273149616 chr9 141213431 17453216 0.12359458924271871 1.3820116393716435 chr10 135534747 22183538 0.16367417574476306 3.70815595025771 chr11 135006516 18474742 0.13684333576906763 0.6572304419080865 chr12 133851895 18233514 0.13622156040450528 0.4405064342340933 chr13 115169878 13832771 0.12010754235582329 0.4047703059015835 chr14 107349540 12565416 0.11705141913044062 0.4175985994018177 chr15 102531392 11507493 0.11223385126771711 0.3926836038772549 chr16 90354753 13110300 0.14509806694950514 1.5075195573812412 chr17 81195210 10767823 0.13261648070126303 0.777962489145605 chr18 78077248 11570296 0.1481903665457061 1.7304729208940233 chr19 59128983 7654805 0.12945943954422487 1.3326543594383267 chr20 63025520 8234099 0.13064706169818194 0.5224346448514452 chr21 48129895 5971267 0.12406565607508598 1.10717614479092 chr22 51304566 4806531 0.09368622278180855 1.2148626329241436 chrMT 16571 481748 29.07175185565144 7.910976494791188 chrX 155270560 11361127 0.07316987199633981 0.40488391716036803 chrY 59373566 5185358 0.08733445452813125 1.7387669146129265