BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084353.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 = 2,172,154 number of mapped reads = 1,967,795 (90.59%) number of supplementary alignments = 13,394 (0.62%) number of secondary alignments = 0 number of mapped bases = 131,833,074 bp number of sequenced bases = 131,786,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,761 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2377 >>>>>>> ACTG content number of A's = 36,736,399 bp (27.88%) number of C's = 25,674,527 bp (19.48%) number of T's = 40,234,830 bp (30.53%) number of G's = 28,981,926 bp (21.99%) number of N's = 158,874 bp (0.12%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,316,041 number of insertions = 9,788 mapped reads with insertion percentage = 0.49% number of deletions = 26,587 mapped reads with deletion percentage = 1.34% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.3485X There is a 3.64% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 5728415 0.022982550563033503 0.5347023529537687 chr2 243199373 9842274 0.04046998098140656 0.36039877245330515 chr3 198022430 11527346 0.05821232473513228 0.2721240424492324 chr4 191154276 6678050 0.03493539427807516 0.22241311589922264 chr5 180915260 8634211 0.04772516702018392 0.24866758459466864 chr6 171115067 6752569 0.03946215326555668 0.23828127755052744 chr7 159138663 10073066 0.06329741503483663 0.5173366812024984 chr8 146364022 3797107 0.025942898726846957 0.3434479502993522 chr9 141213431 4863982 0.03444418824438874 0.3205191267224698 chr10 135534747 5796183 0.042765291766841164 0.2765774067044445 chr11 135006516 9431650 0.06986070213085123 0.41589299435457494 chr12 133851895 5002116 0.037370528075078804 0.2237206169054879 chr13 115169878 3770022 0.032734444678321185 0.2057079415985544 chr14 107349540 4112486 0.03830930248979176 0.24250429306263702 chr15 102531392 5644455 0.055050993553271955 0.26854118686231143 chr16 90354753 6454868 0.07143916380359094 0.3338822794374911 chr17 81195210 2806105 0.034559982048202105 0.26413830011335504 chr18 78077248 2952318 0.03781278254069611 0.7259883803932756 chr19 59128983 3086943 0.05220693547189878 0.4665745058866393 chr20 63025520 2340377 0.03713379913406506 0.23084359774325033 chr21 48129895 1975166 0.04103823621472683 0.24640593497153804 chr22 51304566 1659460 0.03234526923003305 0.2034440799663987 chrMT 16571 122260 7.377949429726631 5.024239486898852 chrX 155270560 8406364 0.054140102283394866 0.29517328325466297 chrY 59373566 375281 0.0063206747595386135 0.13332807690611725