BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008721.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 = 2,313,630 number of mapped reads = 1,620,686 (70.05%) number of supplementary alignments = 6,531 (0.28%) number of secondary alignments = 0 number of mapped bases = 104,691,025 bp number of sequenced bases = 104,633,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,693 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8316 >>>>>>> ACTG content number of A's = 30,885,408 bp (29.52%) number of C's = 18,369,345 bp (17.56%) number of T's = 31,532,866 bp (30.14%) number of G's = 23,816,061 bp (22.76%) number of N's = 29,728 bp (0.03%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,057,048 number of insertions = 8,308 mapped reads with insertion percentage = 0.51% number of deletions = 35,904 mapped reads with deletion percentage = 2.19% homopolymer indels = 47.04% >>>>>>> Coverage mean coverageData = 0.0338X std coverageData = 0.2606X There is a 2.97% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 8511087 0.0341467032894574 0.35400896994681924 chr2 243199373 7274526 0.029911779418937894 0.325058531379515 chr3 198022430 6498882 0.03281891854372255 0.2022539431322801 chr4 191154276 7932820 0.04149956865207661 0.2325922381865266 chr5 180915260 5630246 0.031120901575687976 0.1965274894938712 chr6 171115067 6466631 0.037791125663995444 0.23861491936172632 chr7 159138663 5206910 0.03271932729508982 0.29427490195495243 chr8 146364022 8182991 0.05590848685478184 0.35446944157735893 chr9 141213431 5311218 0.037611280756998246 0.27770356372974697 chr10 135534747 6258662 0.04617754589529724 0.2774731521779056 chr11 135006516 3430957 0.025413269682479624 0.21901095550114846 chr12 133851895 4313489 0.032225834382098216 0.20358995292340568 chr13 115169878 3499971 0.030389638860258236 0.19416312097489308 chr14 107349540 2641118 0.024602974544651053 0.18567398430364132 chr15 102531392 2733025 0.026655494933688212 0.1819886735674757 chr16 90354753 3037942 0.033622381768892665 0.22033153432887867 chr17 81195210 2122864 0.02614518762867908 0.19880962434848268 chr18 78077248 2445343 0.03131953370077798 0.41543472375938445 chr19 59128983 1930423 0.03264766113092119 0.26647359943979243 chr20 63025520 2866216 0.04547707024075327 0.24160413971837627 chr21 48129895 1631400 0.0338957730948717 0.21890224224252244 chr22 51304566 935613 0.01823644702500748 0.14838738659702747 chrMT 16571 31729 1.9147305533763803 1.9318771210355026 chrX 155270560 5549738 0.03574237125183293 0.22476043544527002 chrY 59373566 247224 0.00416387319569116 0.0988338500171031