BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708507.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,995,372 number of mapped reads = 2,014,644 (67.26%) number of supplementary alignments = 489 (0.02%) number of secondary alignments = 0 number of mapped bases = 95,666,982 bp number of sequenced bases = 95,644,727 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,524 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2258 >>>>>>> ACTG content number of A's = 27,109,572 bp (28.34%) number of C's = 17,698,860 bp (18.5%) number of T's = 30,673,161 bp (32.07%) number of G's = 20,161,781 bp (21.08%) number of N's = 1,353 bp (0%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 482,792 number of insertions = 5,172 mapped reads with insertion percentage = 0.26% number of deletions = 14,876 mapped reads with deletion percentage = 0.74% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.2922X There is a 2.64% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% 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% 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 7977333 0.03200526830382501 0.3806896161888986 chr2 243199373 8380940 0.03446119081894179 0.507917366711275 chr3 198022430 6707887 0.03387437978616867 0.21840075339162315 chr4 191154276 6120929 0.032020884534123634 0.21802312627330203 chr5 180915260 6085572 0.03363769313876563 0.21406291234016658 chr6 171115067 5912191 0.034550966806447266 0.2896099615361542 chr7 159138663 5312901 0.033385356517667865 0.3270654406854603 chr8 146364022 4782358 0.03267440956220785 0.4362641314614577 chr9 141213431 4090072 0.028963760536347284 0.2309484939776746 chr10 135534747 4411960 0.03255224285769316 0.22779339412530175 chr11 135006516 4456943 0.033012799174819085 0.2582632951531021 chr12 133851895 4545771 0.03396120017576142 0.21874407333000104 chr13 115169878 3059235 0.026562804902858367 0.2346169882332026 chr14 107349540 3146958 0.02931505808036066 0.20314884023556637 chr15 102531392 2933218 0.0286079993920301 0.2015092840001786 chr16 90354753 2599189 0.028766488908447352 0.20167783869234462 chr17 81195210 2676911 0.032968829072552434 0.2294175889508677 chr18 78077248 2554363 0.0327158431608655 0.31368120084104584 chr19 59128983 1808962 0.030593490843568206 0.30291911171891833 chr20 63025520 1969653 0.031251673925102086 0.2087436641702928 chr21 48129895 1201091 0.02495519676492126 0.1932180526824662 chr22 51304566 1096105 0.021364667620421933 0.17547347478590508 chrMT 16571 97184 5.86470339750166 4.098059380153203 chrX 155270560 3104293 0.01999279837723262 0.1872213570407013 chrY 59373566 634963 0.010694371970179457 0.13185407478899755