BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080795.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 = 3,237,708 number of mapped reads = 2,863,993 (88.46%) number of supplementary alignments = 31,808 (0.98%) number of secondary alignments = 0 number of mapped bases = 203,105,805 bp number of sequenced bases = 203,029,242 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,275 duplication rate = 5.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8562 >>>>>>> ACTG content number of A's = 62,174,889 bp (30.62%) number of C's = 37,574,262 bp (18.51%) number of T's = 62,921,626 bp (30.99%) number of G's = 40,329,288 bp (19.86%) number of N's = 29,177 bp (0.01%) GC percentage = 38.37% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,652,086 number of insertions = 16,356 mapped reads with insertion percentage = 0.57% number of deletions = 42,500 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.02% >>>>>>> Coverage mean coverageData = 0.0656X std coverageData = 0.7187X There is a 3.78% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% 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% 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 14498332 0.0581676865711801 0.7921788656911994 chr2 243199373 18540499 0.0762358009862139 0.58613861069006 chr3 198022430 15080726 0.07615665558694537 0.4302932415027905 chr4 191154276 14605073 0.07640463664019737 0.47679008251966404 chr5 180915260 12836031 0.07095051572763957 0.41606789754218865 chr6 171115067 12167888 0.07110938980025645 0.5007395165905301 chr7 159138663 11471117 0.0720825271731735 0.6283166009733069 chr8 146364022 11468860 0.0783584643499343 2.336619425853096 chr9 141213431 9221924 0.06530486466262547 0.510451094395593 chr10 135534747 9233301 0.0681249731480297 0.6596098763734594 chr11 135006516 8600914 0.06370739913027605 0.45634612894323284 chr12 133851895 10432142 0.07793794775935 0.43902855465224494 chr13 115169878 6174746 0.05361424451626145 0.3648232161152013 chr14 107349540 6579599 0.06129135718699866 0.396879754511217 chr15 102531392 4434438 0.04324956399694642 0.3182230176189884 chr16 90354753 3986259 0.04411786726925146 0.34846997151972503 chr17 81195210 4536052 0.05586600490349123 0.3895849619178358 chr18 78077248 4978012 0.06375752383075797 0.7985852440067966 chr19 59128983 2868389 0.04851071089790264 0.5471364307495226 chr20 63025520 3224735 0.05116554373529961 0.3565530204172185 chr21 48129895 2290420 0.04758830244695111 0.37424571481818936 chr22 51304566 1288924 0.0251229880786829 0.232681129373006 chrMT 16571 102765 6.201496590429063 4.4236571670794795 chrX 155270560 13918178 0.08963822890830045 0.47964609395715196 chrY 59373566 566481 0.009540963060901547 0.283676804995925