BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124801.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 202,938 number of mapped reads = 196,011 (96.59%) number of supplementary alignments = 7,139 (3.52%) number of secondary alignments = 0 number of mapped bases = 25,974,658 bp number of sequenced bases = 25,956,900 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,673 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.6507 >>>>>>> ACTG content number of A's = 7,488,349 bp (28.85%) number of C's = 5,150,550 bp (19.84%) number of T's = 7,115,042 bp (27.41%) number of G's = 6,202,959 bp (23.9%) number of N's = 0 bp (0%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 322,029 number of insertions = 4,770 mapped reads with insertion percentage = 2.26% number of deletions = 8,140 mapped reads with deletion percentage = 3.96% homopolymer indels = 43.95% >>>>>>> Coverage mean coverageData = 0.0084X std coverageData = 5.8525X There is a 0.52% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 7837780 0.031445378023752246 20.067972436808954 chr2 243199373 2716294 0.01116900083455396 4.15849658228443 chr3 198022430 1162609 0.005871097531729107 0.10836765282705701 chr4 191154276 886201 0.00463605114436467 0.3673890207243046 chr5 180915260 1146132 0.006335186982015779 1.536880884846737 chr6 171115067 869582 0.005081855240719393 0.0752930776267628 chr7 159138663 1173303 0.007372834343845154 0.137283867348377 chr8 146364022 1142235 0.007804069500085205 0.13298487903333797 chr9 141213431 713093 0.00504975337650425 0.2763789892222386 chr10 135534747 926704 0.0068373905622887985 0.2540417937588871 chr11 135006516 653558 0.0048409367144916175 0.45609640271378976 chr12 133851895 872504 0.006518428446605108 0.10174292633959121 chr13 115169878 512410 0.004449166821206496 1.0524401461438897 chr14 107349540 583859 0.005438858890312898 0.1703938605749547 chr15 102531392 640427 0.006246155323825117 0.2410598067374248 chr16 90354753 654865 0.007247709481315277 0.1662381057637458 chr17 81195210 471774 0.005810367384972586 0.6671496433494297 chr18 78077248 243408 0.00311752791286906 0.07081369892788156 chr19 59128983 344910 0.0058331799821417524 0.08684682520256953 chr20 63025520 977721 0.015513096916931427 3.468937766451095 chr21 48129895 180300 0.0037461124733390756 0.08054905611157255 chr22 51304566 152996 0.0029821127421680166 0.061294394629165 chrMT 16571 18385 1.109468348319353 1.0975332149602113 chrX 155270560 753898 0.0048553827589724674 0.09221726647721473 chrY 59373566 339710 0.005721569763891224 0.1671791953997828