BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549125.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,903,769 number of mapped reads = 6,317,459 (57.94%) number of secondary alignments = 0 number of mapped bases = 250,742,483 bp number of sequenced bases = 250,715,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 304,794 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1804 >>>>>>> ACTG content number of A's = 73,923,955 bp (29.49%) number of C's = 51,294,998 bp (20.46%) number of T's = 74,221,843 bp (29.6%) number of G's = 51,264,262 bp (20.45%) number of N's = 10,185 bp (0%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 793,293 number of insertions = 6,423 mapped reads with insertion percentage = 0.1% number of deletions = 21,335 mapped reads with deletion percentage = 0.34% homopolymer indels = 44.92% >>>>>>> Coverage mean coverageData = 0.081X std coverageData = 0.9828X There is a 5.94% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 20223663 0.08113786404568275 1.0945098666271182 chr2 243199373 21572401 0.08870253542964521 0.5231049924988503 chr3 198022430 17449380 0.08811819953931481 0.3827694475627165 chr4 191154276 16771100 0.08773593952980681 0.45018511883390716 chr5 180915260 15869754 0.08771926702037186 0.3889520183022347 chr6 171115067 14894969 0.0870465077163544 0.3994742812997832 chr7 159138663 14015459 0.08807073489111819 0.6850659991770414 chr8 146364022 13341624 0.09115371262481431 3.7608513378342128 chr9 141213431 10736639 0.07603128770378789 0.46607939887144484 chr10 135534747 12134915 0.08953360867674767 0.586183916305536 chr11 135006516 11741532 0.08697011335363991 0.47851956125150275 chr12 133851895 11471013 0.08569929473168833 0.3885527934486068 chr13 115169878 8326754 0.07229975532317573 0.34559482692814136 chr14 107349540 7784429 0.07251478674244902 0.41743940937829105 chr15 102531392 7322931 0.07142135552007331 0.33929414386237705 chr16 90354753 6931373 0.07671287641060787 0.3844702616585361 chr17 81195210 6447709 0.07940996765695907 0.38046392645735727 chr18 78077248 6817507 0.0873174602670422 0.8836031711303373 chr19 59128983 4620784 0.0781475304589629 0.8275029832895558 chr20 63025520 5291140 0.0839523418450177 0.4003456402012999 chr21 48129895 3326533 0.06911573357889104 0.4158741448332624 chr22 51304566 2819425 0.054954660370774795 0.312950002342847 chrMT 16571 91798 5.539677750286645 6.786072765978891 chrX 155270560 8330274 0.05365005445977653 0.35243900561094077 chrY 59373566 2409377 0.040579961122766316 0.49088321280473224