BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084364.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 = 2,600,088 number of mapped reads = 2,344,431 (90.17%) number of supplementary alignments = 16,499 (0.63%) number of secondary alignments = 0 number of mapped bases = 157,839,227 bp number of sequenced bases = 157,786,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,623 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0063 >>>>>>> ACTG content number of A's = 43,229,636 bp (27.4%) number of C's = 30,693,511 bp (19.45%) number of T's = 48,385,156 bp (30.66%) number of G's = 35,270,874 bp (22.35%) number of N's = 207,206 bp (0.13%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,574,752 number of insertions = 10,679 mapped reads with insertion percentage = 0.45% number of deletions = 30,166 mapped reads with deletion percentage = 1.27% homopolymer indels = 46.96% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.3485X There is a 4.22% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% 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 15196512 0.06096880296238058 0.537773224509212 chr2 243199373 15080708 0.062009650000207854 0.396804826103765 chr3 198022430 10525176 0.053151433400751624 0.2703374213995323 chr4 191154276 7947431 0.04157600429508571 0.24377903266677606 chr5 180915260 7708830 0.04261017008736576 0.23978857830575875 chr6 171115067 7466412 0.043633866560681064 0.27396635701055067 chr7 159138663 8945825 0.056214026380251796 0.5632052080829262 chr8 146364022 7939134 0.05424238751788332 0.3360466520352607 chr9 141213431 5664491 0.04011297622249543 0.28475310752011834 chr10 135534747 11241653 0.0829429592693304 0.4548322940325616 chr11 135006516 8701287 0.06445086694926636 0.34780181687095807 chr12 133851895 7839206 0.05856626833710498 0.28279016524234163 chr13 115169878 3816511 0.03313810057174846 0.21097782791684117 chr14 107349540 4742255 0.0441758297240957 0.2500989825739215 chr15 102531392 3487359 0.03401259781979747 0.21756957688351103 chr16 90354753 3355187 0.03713348649185063 0.2462177192429753 chr17 81195210 4438818 0.054668471206614284 0.2956076161970241 chr18 78077248 4224950 0.05411243490549257 0.4666994959612544 chr19 59128983 3355453 0.05674802490683799 0.42059830496773265 chr20 63025520 3254869 0.051643667517538926 0.2677488941395792 chr21 48129895 1557501 0.03236036563138149 0.21797951073720265 chr22 51304566 1262106 0.024600266572764692 0.180822005333035 chrMT 16571 6408 0.38669965602558687 0.6977652805284908 chrX 155270560 9755070 0.06282626919101728 0.32518855890223025 chrY 59373566 326075 0.005491922112274678 0.11021770960687181