BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081698.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 = 2,848,205 number of mapped reads = 2,594,635 (91.1%) number of supplementary alignments = 18,388 (0.65%) number of secondary alignments = 0 number of mapped bases = 174,992,727 bp number of sequenced bases = 174,932,819 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,773 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5324 >>>>>>> ACTG content number of A's = 48,173,539 bp (27.54%) number of C's = 33,741,666 bp (19.29%) number of T's = 53,553,170 bp (30.61%) number of G's = 39,462,476 bp (22.56%) number of N's = 1,968 bp (0%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,406,973 number of insertions = 12,474 mapped reads with insertion percentage = 0.48% number of deletions = 33,588 mapped reads with deletion percentage = 1.28% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.3959X There is a 4.72% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13734521 0.05510325689419245 0.5914397248610578 chr2 243199373 14602766 0.06004442289413304 0.49046270715787654 chr3 198022430 12282169 0.06202413029675476 0.2887567523474919 chr4 191154276 11470891 0.0600085503711149 0.3067082212430285 chr5 180915260 10877752 0.060126227052378 0.2834693120819086 chr6 171115067 10342084 0.060439353362144316 0.3259106433859683 chr7 159138663 9704992 0.06098450129620606 0.520006393578743 chr8 146364022 8935082 0.061046983253849094 0.5306320504268742 chr9 141213431 7227376 0.051180514125458786 0.367134122342336 chr10 135534747 8287974 0.06115017870657183 0.46493766524532254 chr11 135006516 7857974 0.058204405482176876 0.35292234612881007 chr12 133851895 8053497 0.06016722437885545 0.2865024929938978 chr13 115169878 5612548 0.04873277715897207 0.25446291912427194 chr14 107349540 5273553 0.049125063786952416 0.26980609777449577 chr15 102531392 4933435 0.048116336897093916 0.2563108179646831 chr16 90354753 4933599 0.05460253983539748 0.30782534191111405 chr17 81195210 4645094 0.0572089658983578 0.3008606469275395 chr18 78077248 4598674 0.05889902779360256 0.6129286733069962 chr19 59128983 3262540 0.05517666353233236 0.5041296860618141 chr20 63025520 3474395 0.05512679625650054 0.2798601274382481 chr21 48129895 2343716 0.04869563916563707 0.2812952209995301 chr22 51304566 1854537 0.03614760136553928 0.2189882878776649 chrMT 16571 25726 1.5524711845996018 1.5768230178342597 chrX 155270560 10194767 0.06565808096525189 0.3246040193356709 chrY 59373566 463065 0.007799177836143444 0.1757293856953876