BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094142.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 = 394,592 number of mapped reads = 368,491 (93.39%) number of supplementary alignments = 20,130 (5.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 185,479 number of mapped paired reads (second in pair) = 183,012 number of mapped paired reads (both in pair) = 363,492 number of mapped paired reads (singletons) = 4,999 number of mapped bases = 46,922,050 bp number of sequenced bases = 45,876,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 345,107 duplication rate = 46.89% >>>>>>> Insert size mean insert size = 460,789.2129 std insert size = 6,329,030.6577 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 45.147 >>>>>>> ACTG content number of A's = 13,053,012 bp (28.45%) number of C's = 9,850,709 bp (21.47%) number of T's = 12,540,535 bp (27.34%) number of G's = 10,431,832 bp (22.74%) number of N's = 533 bp (0%) GC percentage = 44.21% >>>>>>> Mismatches and indels general error rate = 0.038 number of mismatches = 1,714,637 number of insertions = 22,906 mapped reads with insertion percentage = 6.06% number of deletions = 139,481 mapped reads with deletion percentage = 36.45% homopolymer indels = 28.62% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 4.691X 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% 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 1075410 0.004314573001605481 1.4361760267164216 chr2 243199373 1847208 0.007595447213591295 2.2064262009733433 chr3 198022430 1186592 0.005992210074383998 3.7593876068278944 chr4 191154276 2250351 0.011772433487179748 4.711503040064066 chr5 180915260 802812 0.004437502950276278 2.2509149622820805 chr6 171115067 969012 0.0056629262226218805 1.9231831346891979 chr7 159138663 1077574 0.00677128976507739 2.166007573635497 chr8 146364022 978662 0.006686492941550896 2.3274892377367853 chr9 141213431 843992 0.005976711946047115 1.5039311014955865 chr10 135534747 644233 0.004753268178528418 1.2720711148708357 chr11 135006516 1509136 0.01117824564852855 3.5165062180559277 chr12 133851895 1015367 0.007585749906641217 2.030075765751865 chr13 115169878 1086579 0.009434576287386533 4.641789567171175 chr14 107349540 685842 0.006388867618808613 1.292124061417216 chr15 102531392 460703 0.004493287285127271 1.6848843149305694 chr16 90354753 534322 0.0059136014682038916 3.2213551137534746 chr17 81195210 791708 0.009750673715850972 2.9237621599653303 chr18 78077248 438949 0.005621983500238123 2.470056215069528 chr19 59128983 216521 0.0036618421121838 0.507363580432993 chr20 63025520 513750 0.008151459916554436 3.170346335173963 chr21 48129895 516058 0.010722192516729987 3.7986474476824053 chr22 51304566 333474 0.006499889308097841 1.109156850145877 chrMT 16571 4364158 263.36117313378793 1154.0250192362441 chrX 155270560 22616691 0.1456598791168139 12.388041080192979 chrY 59373566 162946 0.0027444199662860066 0.558604683467073