BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013296.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 = 1,671,817 number of mapped reads = 1,323,064 (79.14%) number of supplementary alignments = 12,088 (0.72%) number of secondary alignments = 0 number of mapped bases = 85,244,070 bp number of sequenced bases = 85,209,289 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,814 duplication rate = 8.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0728 >>>>>>> ACTG content number of A's = 23,015,013 bp (27.01%) number of C's = 15,141,708 bp (17.77%) number of T's = 27,843,735 bp (32.68%) number of G's = 19,191,122 bp (22.52%) number of N's = 17,711 bp (0.02%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 711,735 number of insertions = 5,876 mapped reads with insertion percentage = 0.44% number of deletions = 20,872 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2939X There is a 1.84% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.07% 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 5055080 0.020281112960597196 0.3812569214789249 chr2 243199373 6193255 0.02546575233152431 0.37797027391090765 chr3 198022430 9243607 0.04667959584174378 0.30736760342754327 chr4 191154276 5264180 0.027538907892387405 0.23862198567956164 chr5 180915260 4247123 0.023475758761311787 0.2167101640551913 chr6 171115067 7473443 0.043674955870484505 0.32673992028946724 chr7 159138663 3045991 0.019140483793055368 0.2761827747760502 chr8 146364022 3229163 0.02206254621781301 0.2805490294242033 chr9 141213431 2517257 0.017825903543126857 0.23381932590684906 chr10 135534747 3350888 0.024723460766854128 0.30761494925444854 chr11 135006516 2408061 0.017836627974311996 0.2243842231232852 chr12 133851895 3014170 0.022518695009883873 0.2113424878989386 chr13 115169878 2509453 0.021789143511986703 0.21068814400789065 chr14 107349540 3389395 0.03157344689134206 0.25654268202635194 chr15 102531392 2278341 0.02222091162090143 0.2108750752390481 chr16 90354753 1686152 0.018661464328279444 0.2030518901478126 chr17 81195210 2525348 0.03110217954975423 0.25544579931930766 chr18 78077248 1762206 0.022570032181462134 0.4515485303904384 chr19 59128983 1505843 0.02546708777318223 0.3028996647703706 chr20 63025520 1213038 0.019246774957191945 0.19745560982439211 chr21 48129895 1415742 0.029415023656295114 0.24369527170900676 chr22 51304566 645067 0.012573286362075454 0.1510741652331167 chrMT 16571 33554 2.024862711966689 2.1383405942904337 chrX 155270560 10943274 0.07047874368457227 0.4267514362141004 chrY 59373566 294439 0.004959092401490589 0.10083546432527762