BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777243.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 12,384,766 number of mapped reads = 12,185,195 (98.39%) number of supplementary alignments = 120,334 (0.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,115,017 number of mapped paired reads (second in pair) = 6,070,178 number of mapped paired reads (both in pair) = 12,105,412 number of mapped paired reads (singletons) = 79,783 number of mapped bases = 1,194,042,183 bp number of sequenced bases = 1,193,673,920 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 953,789 duplication rate = 4.66% >>>>>>> Insert size mean insert size = 249,130.7159 std insert size = 4,947,844.4904 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 53.2878 >>>>>>> ACTG content number of A's = 348,600,041 bp (29.2%) number of C's = 249,184,218 bp (20.88%) number of T's = 342,444,639 bp (28.69%) number of G's = 253,390,717 bp (21.23%) number of N's = 54,305 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 5,788,243 number of insertions = 126,665 mapped reads with insertion percentage = 1.01% number of deletions = 151,707 mapped reads with deletion percentage = 1.21% homopolymer indels = 42.54% >>>>>>> Coverage mean coverageData = 0.3857X std coverageData = 5.0486X There is a 25.3% of reference with a coverageData >= 1X There is a 8.7% of reference with a coverageData >= 2X There is a 2.02% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 102111379 0.40967351892776227 12.447684997996937 chr2 243199373 112584745 0.4629318883975906 3.315271308852164 chr3 198022430 73782420 0.3725962760885219 1.0818228709335453 chr4 191154276 72237608 0.37790212969130754 4.241063136378902 chr5 180915260 74928359 0.41416273563656264 0.8161888314116633 chr6 171115067 53588723 0.3131736084935174 1.548098743563263 chr7 159138663 82033059 0.5154816400587706 4.9722778118077695 chr8 146364022 56809522 0.3881385686435974 2.738746909179139 chr9 141213431 44258404 0.3134149753786522 4.269966809549539 chr10 135534747 64511845 0.47598011895798203 11.133309795221749 chr11 135006516 68401425 0.506652767781964 2.359727019796813 chr12 133851895 52936967 0.3954891113046999 0.9515977718393283 chr13 115169878 47788889 0.4149426033081324 0.7813847176901332 chr14 107349540 23252881 0.21660904182728682 0.6196150614821911 chr15 102531392 43590117 0.42513922955420325 0.8113143339674707 chr16 90354753 39616369 0.43845362512362795 4.549403990069051 chr17 81195210 33081645 0.40743345574203205 1.5728633164019972 chr18 78077248 25844503 0.33101196138470457 4.512620921649166 chr19 59128983 25343974 0.4286218486118728 6.044586183676667 chr20 63025520 32293181 0.5123826189772016 1.2602028939574075 chr21 48129895 11746938 0.24406739304126884 1.808296780891138 chr22 51304566 11765015 0.22931711380230757 0.6122382660182164 chrMT 16571 605072 36.51390984249593 7.192153678242735 chrX 155270560 36248970 0.23345681241827168 1.1231088048804954 chrY 59373566 4680173 0.07882587008501393 5.20816311825139