BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084338.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 = 2,519,235 number of mapped reads = 1,565,189 (62.13%) number of supplementary alignments = 7,745 (0.31%) number of secondary alignments = 0 number of mapped bases = 99,518,473 bp number of sequenced bases = 99,485,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,981 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6504 >>>>>>> ACTG content number of A's = 27,763,890 bp (27.91%) number of C's = 18,805,197 bp (18.9%) number of T's = 30,400,838 bp (30.56%) number of G's = 22,514,733 bp (22.63%) number of N's = 1,093 bp (0%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 818,091 number of insertions = 7,412 mapped reads with insertion percentage = 0.47% number of deletions = 20,622 mapped reads with deletion percentage = 1.31% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.2463X There is a 2.87% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7480375 0.03001145983102686 0.32257789681655913 chr2 243199373 8680438 0.03569268248072334 0.31779036626106066 chr3 198022430 7291667 0.03682242966112475 0.2096968486285054 chr4 191154276 6297183 0.03294293557942696 0.20409681567251828 chr5 180915260 6158170 0.034038974932241756 0.20216969810285856 chr6 171115067 6090827 0.03559491929486256 0.23478407624568012 chr7 159138663 5286956 0.03322232259799745 0.268964588384954 chr8 146364022 5544376 0.03788073000617597 0.26084883852498547 chr9 141213431 3885118 0.027512383011216546 0.22863489867507508 chr10 135534747 4431307 0.032694988540466305 0.24850455334051205 chr11 135006516 4437155 0.03286622847152059 0.23424591815683635 chr12 133851895 4381760 0.032735883193883805 0.19906085224816583 chr13 115169878 2907376 0.02524423964398052 0.1753152200436276 chr14 107349540 3113388 0.029002341323493327 0.1929253989522745 chr15 102531392 2845987 0.02775722580651202 0.1877551225733566 chr16 90354753 2897343 0.032066304248543516 0.209081935943566 chr17 81195210 2857341 0.03519100449398431 0.2298143741326899 chr18 78077248 2457500 0.031475238471519895 0.44526199865572 chr19 59128983 1795163 0.030360119672614698 0.2842841520296718 chr20 63025520 1731595 0.027474505565364633 0.18514983151473655 chr21 48129895 1372864 0.028524142843029263 0.1919438279769249 chr22 51304566 1065240 0.020763064246562383 0.15775180501381333 chrMT 16571 17737 1.07036388872126 1.230882096588166 chrX 155270560 6250772 0.040257290242271294 0.23311827965004125 chrY 59373566 240835 0.004056266386290492 0.09001135793795877