BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080785.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 = 2,336,868 number of mapped reads = 2,066,064 (88.41%) number of supplementary alignments = 21,893 (0.94%) number of secondary alignments = 0 number of mapped bases = 136,779,040 bp number of sequenced bases = 136,733,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,044 duplication rate = 3.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3322 >>>>>>> ACTG content number of A's = 39,333,705 bp (28.77%) number of C's = 26,386,609 bp (19.3%) number of T's = 41,720,183 bp (30.51%) number of G's = 29,289,874 bp (21.42%) number of N's = 2,837 bp (0%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,009,481 number of insertions = 10,249 mapped reads with insertion percentage = 0.49% number of deletions = 28,813 mapped reads with deletion percentage = 1.38% homopolymer indels = 47.73% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 0.3222X There is a 3.54% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 17462350 0.07005940418499498 0.5070550198764876 chr2 243199373 9958459 0.04094771658806867 0.34793128895619646 chr3 198022430 8578220 0.04331943608610398 0.24950844697518182 chr4 191154276 8366078 0.04376610440040588 0.26010685716409065 chr5 180915260 10642472 0.05882572868645796 0.2926513605527555 chr6 171115067 9565693 0.05590210825794785 0.35299925075967437 chr7 159138663 9836014 0.06180782101958466 0.4348814108519579 chr8 146364022 6241007 0.04264030814895207 0.42967134808687135 chr9 141213431 4645686 0.03289832962135167 0.253441529542425 chr10 135534747 5151703 0.038010201177414674 0.29002390149622015 chr11 135006516 5392517 0.03994264247216038 0.2679363766632241 chr12 133851895 5321940 0.039759915240647134 0.2398834047626716 chr13 115169878 6028209 0.05234188925684197 0.27749254580916227 chr14 107349540 3785574 0.03526399833664867 0.23402833119563976 chr15 102531392 3413831 0.03329547110800953 0.22440510496400495 chr16 90354753 2929215 0.03241904717508331 0.22618883365787948 chr17 81195210 3172247 0.039069385989641506 0.24812229332606095 chr18 78077248 1833922 0.02348855840820619 0.40599123889369776 chr19 59128983 2159091 0.036514935492802235 0.3632835080583679 chr20 63025520 2363474 0.03750026973200697 0.23989259836477875 chr21 48129895 2180363 0.04530163633226293 0.2633156769225569 chr22 51304566 678348 0.013221981061100877 0.1351885104225053 chrMT 16571 108385 6.5406432924989435 4.182541125012545 chrX 155270560 6649799 0.042827172131020844 0.2584090064512942 chrY 59373566 314443 0.005296010012267075 0.1186793953574463