BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081908.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 = 2,539,821 number of mapped reads = 2,337,853 (92.05%) number of supplementary alignments = 17,536 (0.69%) number of secondary alignments = 0 number of mapped bases = 159,722,484 bp number of sequenced bases = 159,659,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,175 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8425 >>>>>>> ACTG content number of A's = 46,038,303 bp (28.84%) number of C's = 30,212,615 bp (18.92%) number of T's = 49,290,165 bp (30.87%) number of G's = 34,116,726 bp (21.37%) number of N's = 1,820 bp (0%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,349,538 number of insertions = 12,347 mapped reads with insertion percentage = 0.52% number of deletions = 35,654 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 0.0516X std coverageData = 0.4655X There is a 4.47% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 12265643 0.049210080002167776 0.8474136165817366 chr2 243199373 14342317 0.058973494968673296 0.5376781673290869 chr3 198022430 10709420 0.05408185325268456 0.26271962636387736 chr4 191154276 10670612 0.05582198956407337 0.3026595422010667 chr5 180915260 10414456 0.05756538171517427 0.26904603490829865 chr6 171115067 8244615 0.04818170103045338 0.2709549612417568 chr7 159138663 9237959 0.05804974621409255 0.6561711122113364 chr8 146364022 7642874 0.05221825620506657 0.6286692805551295 chr9 141213431 6805396 0.048192271456105336 0.4352675268567307 chr10 135534747 7260647 0.053570373359681706 0.5390560612171591 chr11 135006516 7400178 0.05481348766899518 0.36714562974064713 chr12 133851895 6656199 0.049728089393131114 0.25165989619599943 chr13 115169878 5388294 0.04678561871881118 0.23921785307866078 chr14 107349540 5121096 0.04770487139488441 0.26743425145033867 chr15 102531392 4627876 0.04513618619359035 0.23966539292835531 chr16 90354753 4442466 0.04916693203732182 0.31187189627070755 chr17 81195210 3952426 0.04867806857079377 0.2682621478275772 chr18 78077248 4291503 0.054964834313832374 0.8612353995152863 chr19 59128983 3013191 0.050959628377169955 0.64779905251777 chr20 63025520 3141980 0.04985250419195272 0.26361088396692955 chr21 48129895 2147910 0.04462735686416935 0.27287214750384486 chr22 51304566 1664238 0.03243839934246788 0.19784228040089405 chrMT 16571 16632 1.0036811296843884 1.2431407336257083 chrX 155270560 9813403 0.06320195534813554 0.3138457319396496 chrY 59373566 451153 0.007598549832765645 0.20331695094250773