BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238263.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,485,513 number of mapped reads = 1,163,420 (78.32%) number of supplementary alignments = 12,789 (0.86%) number of secondary alignments = 0 number of mapped bases = 74,364,948 bp number of sequenced bases = 74,316,634 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,522 duplication rate = 9.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1012 >>>>>>> ACTG content number of A's = 20,515,788 bp (27.61%) number of C's = 14,322,834 bp (19.27%) number of T's = 22,832,499 bp (30.72%) number of G's = 16,629,055 bp (22.38%) number of N's = 16,458 bp (0.02%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 752,242 number of insertions = 6,014 mapped reads with insertion percentage = 0.51% number of deletions = 29,373 mapped reads with deletion percentage = 2.49% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.024X std coverageData = 0.2783X There is a 1.48% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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% 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 5445015 0.021845542362761053 0.32336352879856944 chr2 243199373 6302148 0.025913504308253295 0.33573429806192895 chr3 198022430 4845687 0.024470394591158184 0.23277012256165558 chr4 191154276 4577804 0.02394821657036853 0.2519598278407701 chr5 180915260 4876894 0.026956786287679658 0.24587715745437383 chr6 171115067 4402893 0.02573059799579192 0.28129629726965183 chr7 159138663 4755346 0.029881776749626204 0.3860851014626028 chr8 146364022 3733310 0.0255070197510697 0.33249998937530634 chr9 141213431 2903032 0.02055776125147756 0.24668850653916113 chr10 135534747 3176130 0.02343406447646964 0.26324219871085835 chr11 135006516 3073235 0.022763604980369983 0.2444787355675994 chr12 133851895 3330484 0.024881859162322655 0.2373873683430607 chr13 115169878 2765915 0.024015958408847148 0.23686468876622838 chr14 107349540 2650170 0.024687297216178104 0.28214054373922437 chr15 102531392 2186659 0.021326726940369637 0.2788452456336084 chr16 90354753 2148822 0.023782058260952803 0.23554122882312115 chr17 81195210 1998499 0.024613508604756366 0.24123379254218752 chr18 78077248 1964688 0.02516338690625981 0.3397131085558595 chr19 59128983 1329489 0.022484557192536187 0.2789049579220899 chr20 63025520 1450964 0.02302184892722821 0.22843617945773284 chr21 48129895 951146 0.019762062643186733 0.21313758457758794 chr22 51304566 924949 0.018028590281808445 0.19953310158754714 chrMT 16571 9948 0.6003258704966508 1.1695801357415418 chrX 155270560 4359535 0.02807702245680057 0.2657777097543068 chrY 59373566 202186 0.0034053201385950103 0.10418508940620996