BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819046.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,989,240 number of mapped reads = 1,270,952 (63.89%) number of supplementary alignments = 6,451 (0.32%) number of secondary alignments = 0 number of mapped bases = 71,570,314 bp number of sequenced bases = 71,550,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,043 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7304 >>>>>>> ACTG content number of A's = 18,019,452 bp (25.18%) number of C's = 14,479,542 bp (20.24%) number of T's = 21,836,916 bp (30.52%) number of G's = 17,213,351 bp (24.06%) number of N's = 1,623 bp (0%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 356,799 number of insertions = 4,781 mapped reads with insertion percentage = 0.37% number of deletions = 11,650 mapped reads with deletion percentage = 0.91% homopolymer indels = 39.97% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.1982X There is a 2.12% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7976984 0.032003868106711755 0.282176729861961 chr2 243199373 5970575 0.02455012497092252 0.2241085139170109 chr3 198022430 4714274 0.023806767748481825 0.1658266254946542 chr4 191154276 4572132 0.023918544202484907 0.17902978929840738 chr5 180915260 3548857 0.01961612856759568 0.1519492828206912 chr6 171115067 3749926 0.02191464530706697 0.1661398859667176 chr7 159138663 3103843 0.01950401581544015 0.1738797463096991 chr8 146364022 4455291 0.0304397961952699 0.2089775857151601 chr9 141213431 2622059 0.018568056745253927 0.20356969748813875 chr10 135534747 3406632 0.025134750131639676 0.21788206234273808 chr11 135006516 2276989 0.016865771130631948 0.18336650454060316 chr12 133851895 3235207 0.02417005003926168 0.17063287402510813 chr13 115169878 2206183 0.01915590290023577 0.1473060583739122 chr14 107349540 2514642 0.02342480461490566 0.17560154530263597 chr15 102531392 2079581 0.020282383369963415 0.15372538514877934 chr16 90354753 2130596 0.023580342253826977 0.17955374884868847 chr17 81195210 1633583 0.020119204076201047 0.17150757884182047 chr18 78077248 1734371 0.02221352627592612 0.3509130642431382 chr19 59128983 1427058 0.02413466167682945 0.2269479316336642 chr20 63025520 2200868 0.03492026721873933 0.2052542112837723 chr21 48129895 912629 0.018961790795512853 0.1581562531157369 chr22 51304566 862412 0.01680965393996316 0.13949710415901778 chrMT 16571 1383 0.08345905497555971 0.3145512637935008 chrX 155270560 4030571 0.02595837227610952 0.19061923302742986 chrY 59373566 203668 0.0034302807414329805 0.08511838433610605