BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094032.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 = 382,794 number of mapped reads = 363,426 (94.94%) number of supplementary alignments = 19,517 (5.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,589 number of mapped paired reads (second in pair) = 180,837 number of mapped paired reads (both in pair) = 360,134 number of mapped paired reads (singletons) = 3,292 number of mapped bases = 46,929,241 bp number of sequenced bases = 46,026,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 337,858 duplication rate = 47.3% >>>>>>> Insert size mean insert size = 792,703.9257 std insert size = 8,073,090.0641 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 44.6599 >>>>>>> ACTG content number of A's = 12,743,696 bp (27.69%) number of C's = 10,223,947 bp (22.21%) number of T's = 12,271,941 bp (26.66%) number of G's = 10,786,062 bp (23.43%) number of N's = 538 bp (0%) GC percentage = 45.65% >>>>>>> Mismatches and indels general error rate = 0.0359 number of mismatches = 1,585,822 number of insertions = 29,330 mapped reads with insertion percentage = 7.95% number of deletions = 117,596 mapped reads with deletion percentage = 31.22% homopolymer indels = 28.48% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 4.2885X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% 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% 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 612254 0.0024563790354608585 0.8826311400824183 chr2 243199373 3418509 0.014056405482591438 4.617255437734391 chr3 198022430 606716 0.0030638751377811088 0.7397436368142578 chr4 191154276 718754 0.0037600728324800855 0.9237130167713097 chr5 180915260 481899 0.002663672484012681 0.8550128560361057 chr6 171115067 1037598 0.006063744228905337 2.592355899845534 chr7 159138663 1443578 0.009071195979571602 2.491133189999342 chr8 146364022 1033463 0.007060908725233035 2.4322811334258154 chr9 141213431 637707 0.004515908971859766 1.4772003543215455 chr10 135534747 747890 0.005518068366630735 1.422132211750638 chr11 135006516 1141119 0.00845232536776225 2.5205999447079646 chr12 133851895 1409685 0.010531677567956733 2.8073703195381903 chr13 115169878 794792 0.006901040565485361 2.1541269395853906 chr14 107349540 259137 0.0024139553835069998 0.6381336493144123 chr15 102531392 577849 0.0056358251724505995 1.3126880005293045 chr16 90354753 190701 0.0021105807239603655 0.4634758440464225 chr17 81195210 1028692 0.012669368057549207 2.8779720320892577 chr18 78077248 197057 0.0025238722553335897 0.7032129740535623 chr19 59128983 433694 0.007334710965686659 2.196756139900651 chr20 63025520 904019 0.014343697600591 5.509693419213506 chr21 48129895 270787 0.005626170595219458 1.8329097483308197 chr22 51304566 178710 0.003483315695526983 0.9918553806380471 chrMT 16571 4906130 296.06722587653127 1232.5816769576718 chrX 155270560 22686612 0.14611019629220118 8.781856988328315 chrY 59373566 1211889 0.02041125506930138 7.289383994652636