BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081176.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 = 2,359,698 number of mapped reads = 2,083,848 (88.31%) number of supplementary alignments = 16,819 (0.71%) number of secondary alignments = 0 number of mapped bases = 139,535,227 bp number of sequenced bases = 139,473,816 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,095 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9407 >>>>>>> ACTG content number of A's = 38,965,934 bp (27.94%) number of C's = 25,646,252 bp (18.39%) number of T's = 43,915,692 bp (31.49%) number of G's = 30,904,904 bp (22.16%) number of N's = 41,034 bp (0.03%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,217,827 number of insertions = 11,511 mapped reads with insertion percentage = 0.55% number of deletions = 37,791 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.4629X There is a 3.97% of reference with a coverageData >= 1X There is a 0.38% 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% 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 11403043 0.04574930627755588 0.9288426180196979 chr2 243199373 12244402 0.05034717749868541 0.5179507925531758 chr3 198022430 9489419 0.047920929967377936 0.23885966953443308 chr4 191154276 9479643 0.049591582246373604 0.2579101371993289 chr5 180915260 9041699 0.04997753644441049 0.2481587991871594 chr6 171115067 8304819 0.048533534454917406 0.329833629164256 chr7 159138663 8140919 0.051156135451508725 0.7936709422243851 chr8 146364022 7333897 0.05010723878577209 0.5388568541302218 chr9 141213431 6099530 0.04319369593109029 0.3964736245129632 chr10 135534747 6581731 0.04856120770270077 0.3737183937857988 chr11 135006516 6313575 0.04676496503324328 0.3845566139688667 chr12 133851895 6555977 0.04897933645242751 0.2508385480953444 chr13 115169878 4576686 0.03973856775293276 0.21826130155564094 chr14 107349540 4449992 0.04145329360517055 0.24874654811006033 chr15 102531392 4142527 0.040402523746093294 0.22779450057472303 chr16 90354753 3923707 0.04342557385996064 0.2651700699066307 chr17 81195210 3690414 0.045451129444704925 0.2944270531568109 chr18 78077248 3767890 0.04825848882378641 0.7755872211410505 chr19 59128983 2697874 0.045626930535909944 0.5969340312718987 chr20 63025520 2802366 0.044463988555746944 0.24973749840152365 chr21 48129895 1912718 0.03974074740865319 0.23882174975747555 chr22 51304566 1481329 0.028873239079734152 0.184434440920301 chrMT 16571 28631 1.7277774425200652 1.6872000411300807 chrX 155270560 4783646 0.030808454609811416 0.23380724340574852 chrY 59373566 288793 0.004863999578532978 0.12303787521692534