BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236074.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 = 2,756,352 number of mapped reads = 2,330,571 (84.55%) number of supplementary alignments = 20,553 (0.75%) number of secondary alignments = 0 number of mapped bases = 152,335,868 bp number of sequenced bases = 152,247,797 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,069 duplication rate = 6.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4909 >>>>>>> ACTG content number of A's = 42,148,563 bp (27.68%) number of C's = 26,619,927 bp (17.48%) number of T's = 49,995,504 bp (32.84%) number of G's = 33,416,979 bp (21.95%) number of N's = 66,824 bp (0.04%) GC percentage = 39.43% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,306,273 number of insertions = 10,930 mapped reads with insertion percentage = 0.47% number of deletions = 50,708 mapped reads with deletion percentage = 2.15% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.4918X There is a 3.47% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.09% 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 0.01% 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 15115625 0.060644282206221665 0.715877783819894 chr2 243199373 13363214 0.05494756764853995 0.5099591387055252 chr3 198022430 16017532 0.08088746310203344 0.38258567415141964 chr4 191154276 7317195 0.038279002453494686 0.2861379371412225 chr5 180915260 7215184 0.03988156665170202 0.2664166715104342 chr6 171115067 6857767 0.04007693255907149 0.28961413619511167 chr7 159138663 13387409 0.08412417666221061 1.0485863110224443 chr8 146364022 11939296 0.08157261488755754 0.8712055986930808 chr9 141213431 5144136 0.03642809301899902 0.35614814415646984 chr10 135534747 3655835 0.02697341516415713 0.47018433949752453 chr11 135006516 9690283 0.0717764096660342 0.4211119741160894 chr12 133851895 5247316 0.03920240352219145 0.26686981530375503 chr13 115169878 5569910 0.04836255882809913 0.2916285874820512 chr14 107349540 5164460 0.04810882282308802 0.29778959712627234 chr15 102531392 4998620 0.048752093407646316 0.2924239036024007 chr16 90354753 3447392 0.03815396407535971 0.28991738767093217 chr17 81195210 2774725 0.03417350604795529 0.3148426016997046 chr18 78077248 1348355 0.0172694995602304 0.5340118155788222 chr19 59128983 744240 0.01258672079646626 0.5810086268285958 chr20 63025520 2657255 0.0421615720108299 0.2806406579975935 chr21 48129895 3959913 0.08227553789593765 0.40011919063116175 chr22 51304566 893209 0.017409931895730296 0.1677683505115624 chrMT 16571 233810 14.10958904109589 8.96861719635852 chrX 155270560 5230504 0.03368638588023383 0.2627258381888511 chrY 59373566 362683 0.006108492792903832 0.17974942661972643