BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094101.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 353,754 number of mapped reads = 331,717 (93.77%) number of supplementary alignments = 22,761 (6.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 166,860 number of mapped paired reads (second in pair) = 164,857 number of mapped paired reads (both in pair) = 328,278 number of mapped paired reads (singletons) = 3,439 number of mapped bases = 40,467,942 bp number of sequenced bases = 39,650,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,238 duplication rate = 50.26% >>>>>>> Insert size mean insert size = 1,610,631.3876 std insert size = 11,325,693.1062 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 40.0941 >>>>>>> ACTG content number of A's = 11,472,328 bp (28.93%) number of C's = 8,456,819 bp (21.33%) number of T's = 10,712,643 bp (27.02%) number of G's = 9,008,698 bp (22.72%) number of N's = 402 bp (0%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0368 number of mismatches = 1,408,576 number of insertions = 26,005 mapped reads with insertion percentage = 7.72% number of deletions = 112,988 mapped reads with deletion percentage = 32.77% homopolymer indels = 28.22% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 2.7035X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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% 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 1187323 0.004763570879929724 1.8361012247448756 chr2 243199373 1778704 0.0073137688558103315 2.163054275399999 chr3 198022430 712264 0.0035968854639345654 1.2870912664934662 chr4 191154276 1652402 0.008644337100782407 2.346703057570795 chr5 180915260 795116 0.004394963697368591 1.8587160885124718 chr6 171115067 812134 0.004746127937407172 1.4307225944457016 chr7 159138663 996309 0.006260634475733907 1.8711447584615437 chr8 146364022 821428 0.005612226206792814 1.470737771933811 chr9 141213431 933311 0.006609222602912325 2.9308843584734157 chr10 135534747 762200 0.005623650147810436 1.8343075378024039 chr11 135006516 1221497 0.009047689224126042 2.25556085333703 chr12 133851895 942818 0.0070437403968020024 1.7154210880961067 chr13 115169878 539769 0.004686720255100036 1.1314026949800646 chr14 107349540 205455 0.0019138880334279961 0.7410315819158694 chr15 102531392 340389 0.0033198515436131015 0.7019660113438226 chr16 90354753 199566 0.002208693990896085 0.9468613216154874 chr17 81195210 272811 0.0033599395826428677 0.7848691477817117 chr18 78077248 327177 0.004190426896193882 1.1735544414256316 chr19 59128983 99335 0.001679971394062367 0.563830925387398 chr20 63025520 211897 0.003362082534186152 1.0765346286473079 chr21 48129895 167149 0.003472872733256534 1.3001140217908036 chr22 51304566 39893 7.775721170704378E-4 0.24027947981298026 chrMT 16571 200599 12.105425140305353 65.59855212072466 chrX 155270560 24640557 0.1586943268575833 9.376747449691452 chrY 59373566 607839 0.010237535673703682 2.1264766435335516