BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046536.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 10,327,296 number of mapped reads = 10,135,817 (98.15%) number of supplementary alignments = 47,496 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,153,649 number of mapped paired reads (second in pair) = 4,982,168 number of mapped paired reads (both in pair) = 9,956,880 number of mapped paired reads (singletons) = 178,937 number of mapped bases = 996,169,130 bp number of sequenced bases = 995,896,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,649,288 duplication rate = 33.25% >>>>>>> Insert size mean insert size = 29,635.8439 std insert size = 1,732,062.2501 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 53.7294 >>>>>>> ACTG content number of A's = 290,140,562 bp (29.13%) number of C's = 208,311,861 bp (20.92%) number of T's = 290,786,353 bp (29.2%) number of G's = 206,562,485 bp (20.74%) number of N's = 94,890 bp (0.01%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 4,356,365 number of insertions = 87,440 mapped reads with insertion percentage = 0.84% number of deletions = 95,677 mapped reads with deletion percentage = 0.92% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.3218X std coverageData = 19.4812X There is a 4.85% of reference with a coverageData >= 1X There is a 1.97% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 145202587 0.5825565706414028 29.890414242223496 chr2 243199373 82426224 0.3389244922107591 15.788594944300133 chr3 198022430 62985525 0.3180726799484281 15.451605120597845 chr4 191154276 33939785 0.17755179591169595 8.903938959304131 chr5 180915260 78196404 0.43222668999840036 25.495794693332428 chr6 171115067 72501507 0.4237003103882138 19.18172181902412 chr7 159138663 43628819 0.2741559981561489 13.983046794943375 chr8 146364022 65602767 0.4482164817799281 20.245666436188674 chr9 141213431 19598790 0.13878842728493723 7.543610481944453 chr10 135534747 50940703 0.37584976640713397 31.03465961487682 chr11 135006516 24466870 0.18122732683509885 7.859455994208774 chr12 133851895 31431719 0.23482460969267563 13.644507545752194 chr13 115169878 29682051 0.25772408129146407 17.334717138097805 chr14 107349540 61803338 0.5757205666647477 38.46035453033226 chr15 102531392 16773015 0.16358906938472073 8.048403731171554 chr16 90354753 41365495 0.45781205334045905 24.007814072958322 chr17 81195210 49857804 0.6140485873489335 25.19687153727508 chr18 78077248 13017464 0.16672544606080378 9.296077434855311 chr19 59128983 10786693 0.18242649294340138 8.577661785386013 chr20 63025520 13498551 0.21417595602543224 11.121371440926765 chr21 48129895 7308957 0.15185898494064864 15.893169598149118 chr22 51304566 10283008 0.20043065952453432 11.742789593643204 chrMT 16571 63429 3.8277110614929697 2.393287266412931 chrX 155270560 30565700 0.19685444555619558 16.785388305321273 chrY 59373566 241925 0.004074624724410186 0.30522554096802024