BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231804.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 = 12,349,481 number of mapped reads = 10,256,843 (83.05%) number of supplementary alignments = 103,956 (0.84%) number of secondary alignments = 0 number of mapped bases = 664,628,245 bp number of sequenced bases = 664,385,198 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,079,031 duplication rate = 7.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.274 >>>>>>> ACTG content number of A's = 192,745,716 bp (29.01%) number of C's = 134,627,977 bp (20.26%) number of T's = 191,576,233 bp (28.84%) number of G's = 145,384,909 bp (21.88%) number of N's = 50,363 bp (0.01%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 3,843,707 number of insertions = 47,769 mapped reads with insertion percentage = 0.46% number of deletions = 144,397 mapped reads with deletion percentage = 1.39% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.2147X std coverageData = 8.8311X There is a 12.37% of reference with a coverageData >= 1X There is a 4.82% of reference with a coverageData >= 2X There is a 2% of reference with a coverageData >= 3X There is a 0.87% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 63573098 0.2550569292262666 3.0299252010319573 chr2 243199373 41507571 0.1706730181413749 31.056450123706703 chr3 198022430 66001359 0.3333024395266738 0.8978840025986287 chr4 191154276 19684809 0.10297864851320407 0.8169111092530407 chr5 180915260 29275899 0.1618210592074986 0.6301520264932046 chr6 171115067 51837435 0.30293904510466046 1.361614846353449 chr7 159138663 41189756 0.2588293455751856 2.3859100116078094 chr8 146364022 46865931 0.3202011693830059 2.0196691702692733 chr9 141213431 35420313 0.25082821619141876 1.2610917807420263 chr10 135534747 38300413 0.28258740911657143 1.5959077802936175 chr11 135006516 30930430 0.2291032382466636 1.4478816499331988 chr12 133851895 15079788 0.11266025034610082 0.5740421446735857 chr13 115169878 18887667 0.16399832428406325 0.6139679296824615 chr14 107349540 29353797 0.27344129280852064 0.9392360654545997 chr15 102531392 9277124 0.0904808158656424 0.4549006412986122 chr16 90354753 20926724 0.2316062332658914 0.9384538555196874 chr17 81195210 17747832 0.2185822538053661 0.8691718145100215 chr18 78077248 8450891 0.10823756236900153 2.9560551045064076 chr19 59128983 19974036 0.3378044909042322 1.9745921680546095 chr20 63025520 12788762 0.2029140259374298 0.7668187528980108 chr21 48129895 11380844 0.2364610186662572 0.9052466889406019 chr22 51304566 10067311 0.1962264138439452 0.672460432570334 chrMT 16571 603639 36.42743346810693 21.494628635537662 chrX 155270560 23922552 0.15407010833219123 0.8266737905423422 chrY 59373566 1580264 0.026615615440716497 0.6807848391556469