BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237333.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 = 3,259,342 number of mapped reads = 3,029,625 (92.95%) number of supplementary alignments = 19,301 (0.59%) number of secondary alignments = 0 number of mapped bases = 194,267,574 bp number of sequenced bases = 194,162,938 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 267,077 duplication rate = 7.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4966 >>>>>>> ACTG content number of A's = 52,421,977 bp (27%) number of C's = 34,054,271 bp (17.54%) number of T's = 63,758,411 bp (32.84%) number of G's = 43,906,654 bp (22.61%) number of N's = 21,625 bp (0.01%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,150,968 number of insertions = 13,755 mapped reads with insertion percentage = 0.45% number of deletions = 58,641 mapped reads with deletion percentage = 1.91% homopolymer indels = 43.22% >>>>>>> Coverage mean coverageData = 0.0628X std coverageData = 0.7092X There is a 5.01% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 16048635 0.0643875426894122 1.2499968293235426 chr2 243199373 12224031 0.05026341494720877 0.8963141895263563 chr3 198022430 18017530 0.0909873189617964 0.3629780221545487 chr4 191154276 9870031 0.051633848881308834 0.3761626822499979 chr5 180915260 13106981 0.07244817822443501 0.3294769160819469 chr6 171115067 8990834 0.05254262034096623 0.42217418280680863 chr7 159138663 12566937 0.07896847166549338 0.8397950816852054 chr8 146364022 13021194 0.08896444510113284 1.6162325707654186 chr9 141213431 9070454 0.0642322329807283 0.5694554728874018 chr10 135534747 10753820 0.07934363872018738 0.7757456757225273 chr11 135006516 5648712 0.04184029161970226 0.33985393084779775 chr12 133851895 7695180 0.05749025816929973 0.3233039283711319 chr13 115169878 7624853 0.06620527113869132 0.3244675364813485 chr14 107349540 6984957 0.0650674143550126 0.3370012168064158 chr15 102531392 4224464 0.041201664364412416 0.26396121849534837 chr16 90354753 2920765 0.03232552691500357 0.3098230012525164 chr17 81195210 4224075 0.052023696964389896 0.34656980670928605 chr18 78077248 5014395 0.06422351105407814 1.0117745360538948 chr19 59128983 3949050 0.06678704418102371 0.8245207438489629 chr20 63025520 3694505 0.05861919108323105 0.30394765594516676 chr21 48129895 2476939 0.051463627751525326 0.3351173330124839 chr22 51304566 1039013 0.020251862183182683 0.16597597753892934 chrMT 16571 13547 0.8175125218755658 1.1649933383574425 chrX 155270560 14533535 0.09360135623907069 0.42802373470288374 chrY 59373566 553137 0.009316216580287598 0.29495304098450703