BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081112.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 = 2,821,357 number of mapped reads = 2,562,295 (90.82%) number of supplementary alignments = 13,962 (0.49%) number of secondary alignments = 0 number of mapped bases = 171,300,639 bp number of sequenced bases = 171,231,196 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,755 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.252 >>>>>>> ACTG content number of A's = 46,170,735 bp (26.96%) number of C's = 33,271,771 bp (19.43%) number of T's = 52,072,418 bp (30.41%) number of G's = 39,714,418 bp (23.19%) number of N's = 1,854 bp (0%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,548,855 number of insertions = 13,519 mapped reads with insertion percentage = 0.52% number of deletions = 38,170 mapped reads with deletion percentage = 1.47% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.0553X std coverageData = 0.5471X There is a 4.57% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13711312 0.055010141780148264 0.8600764047093552 chr2 243199373 12497001 0.051385827380402004 0.5801993657138782 chr3 198022430 14421495 0.07282758321872931 0.3137253882088034 chr4 191154276 10870355 0.05686692041354074 0.3518049742256574 chr5 180915260 9082855 0.050205024164351866 0.26272813829763253 chr6 171115067 13359838 0.07807517031799427 0.6338534195915003 chr7 159138663 9672047 0.06077748057993927 0.9083795280879754 chr8 146364022 13234065 0.09041883940576599 0.5155044180609843 chr9 141213431 7325192 0.051873196112627556 0.6339962139812747 chr10 135534747 6328212 0.046690698437648614 0.4820869939605852 chr11 135006516 8609694 0.06377243302834361 0.5128566482495898 chr12 133851895 8449342 0.0631245601715239 0.3194593314232495 chr13 115169878 4153641 0.0360653416685915 0.21575152953919782 chr14 107349540 4949069 0.0461023773366891 0.3696250027928094 chr15 102531392 4559827 0.04447249677445128 0.2673597667864225 chr16 90354753 5121299 0.05667990703267154 0.3905868423688514 chr17 81195210 4321441 0.05322285637293136 0.31206009882462343 chr18 78077248 3820249 0.04892909391478552 1.2368775647982306 chr19 59128983 4264779 0.07212670984041786 0.6709419332079632 chr20 63025520 2633665 0.041787279184685826 0.2718608781355721 chr21 48129895 3151358 0.06547610378123617 0.414213010423382 chr22 51304566 2033213 0.039630254352020056 0.22820916092683585 chrMT 16571 149924 9.047371914790899 5.358994514596487 chrX 155270560 4099019 0.026399202785125524 0.2734543615218044 chrY 59373566 481747 0.008113829646007787 0.243770647851358