BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013277.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,509,298 number of mapped reads = 2,270,161 (90.47%) number of supplementary alignments = 18,464 (0.74%) number of secondary alignments = 0 number of mapped bases = 148,102,463 bp number of sequenced bases = 148,046,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,420 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.151 >>>>>>> ACTG content number of A's = 40,857,379 bp (27.6%) number of C's = 28,845,816 bp (19.48%) number of T's = 44,321,157 bp (29.94%) number of G's = 33,989,105 bp (22.96%) number of N's = 33,282 bp (0.02%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,171,305 number of insertions = 10,663 mapped reads with insertion percentage = 0.47% number of deletions = 32,135 mapped reads with deletion percentage = 1.4% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 0.0478X std coverageData = 0.3925X There is a 4.27% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 10675880 0.04283190933353783 0.5271510706224631 chr2 243199373 16077060 0.06610650266766929 0.5112539542013242 chr3 198022430 9233808 0.04663011154847459 0.2339374544843182 chr4 191154276 9329691 0.048807126867515115 0.24600098057171746 chr5 180915260 7040773 0.038917518621701674 0.21548752181718558 chr6 171115067 8411267 0.04915561877435375 0.3159249596391302 chr7 159138663 9130993 0.05737759025913144 0.8402085164550033 chr8 146364022 8628281 0.05895083287612853 0.36121684537459975 chr9 141213431 4726157 0.033468183348650454 0.3220475960799744 chr10 135534747 6999354 0.05164250610952186 0.38611325274022223 chr11 135006516 5975400 0.04426008593540774 0.3157803380237666 chr12 133851895 7340367 0.05483947014721009 0.25800929922571986 chr13 115169878 3273512 0.028423334788980154 0.1869339488577114 chr14 107349540 5066816 0.04719923345735808 0.26764394681972037 chr15 102531392 4496599 0.04385582710122574 0.23365519934234102 chr16 90354753 5119575 0.05666082668611799 0.2805511813324057 chr17 81195210 3799270 0.046791799664044224 0.2677716487223754 chr18 78077248 3557242 0.04556054537168113 0.639423990503731 chr19 59128983 3121397 0.05278962771945528 0.44859018713306076 chr20 63025520 3301504 0.05238360587901536 0.25381231098224255 chr21 48129895 2608449 0.05419602515235074 0.27108263070882066 chr22 51304566 1410177 0.027486383960445157 0.17902290168814516 chrMT 16571 343138 20.707138977732182 15.857081566527722 chrX 155270560 8104882 0.05219844637644123 0.27684453794405794 chrY 59373566 330871 0.005572698800001334 0.1058440555171669