BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082946.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 = 2,054,837 number of mapped reads = 1,900,811 (92.5%) number of supplementary alignments = 21,872 (1.06%) number of secondary alignments = 0 number of mapped bases = 128,501,759 bp number of sequenced bases = 128,452,259 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,468 duplication rate = 4.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4201 >>>>>>> ACTG content number of A's = 36,206,747 bp (28.19%) number of C's = 23,234,419 bp (18.09%) number of T's = 41,460,055 bp (32.28%) number of G's = 27,544,889 bp (21.44%) number of N's = 6,149 bp (0%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 913,247 number of insertions = 10,779 mapped reads with insertion percentage = 0.56% number of deletions = 30,250 mapped reads with deletion percentage = 1.58% homopolymer indels = 49.23% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.3192X There is a 3.43% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% 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 11566702 0.04640591045909571 0.44127465529488213 chr2 243199373 13240781 0.054444141186169914 0.4731985713912097 chr3 198022430 9150818 0.046211017610479785 0.24996168922019854 chr4 191154276 9199196 0.048124458382505654 0.26199915894116865 chr5 180915260 6556581 0.03624117169552198 0.22363681001179583 chr6 171115067 8794335 0.05139427611012185 0.3356211324219265 chr7 159138663 7567058 0.047550091582709855 0.33007131744098817 chr8 146364022 10331312 0.07058641774684218 0.4551380003455199 chr9 141213431 3654114 0.02587653294820094 0.29567894794717486 chr10 135534747 4544359 0.03352910674633126 0.23773994348881838 chr11 135006516 4974154 0.03684380685744087 0.27668101196323097 chr12 133851895 3987445 0.029789977945400024 0.20510145498607119 chr13 115169878 2986547 0.0259316676535856 0.1899030232758271 chr14 107349540 2848598 0.02653572618941823 0.203363962609475 chr15 102531392 2198044 0.021437766103867974 0.17596720464341978 chr16 90354753 4833835 0.053498403122191035 0.2817565945722242 chr17 81195210 2989318 0.036816432890560906 0.24323765209818696 chr18 78077248 4765064 0.06103012237316561 0.5477583179066547 chr19 59128983 1655464 0.027997505047566942 0.3335118450200317 chr20 63025520 2347279 0.03724331032889534 0.2299706201222195 chr21 48129895 2886159 0.05996603566245054 0.2903266596245191 chr22 51304566 1648113 0.032124099831582244 0.20656018023229708 chrMT 16571 149091 8.997103373363105 5.738562783376694 chrX 155270560 5420526 0.034910198043982064 0.23911974214213952 chrY 59373566 206866 0.003484143094925442 0.08033586005538203