BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094108.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 = 374,492 number of mapped reads = 352,340 (94.08%) number of supplementary alignments = 26,967 (7.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 177,194 number of mapped paired reads (second in pair) = 175,146 number of mapped paired reads (both in pair) = 349,166 number of mapped paired reads (singletons) = 3,174 number of mapped bases = 42,268,601 bp number of sequenced bases = 41,238,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 340,021 duplication rate = 53.19% >>>>>>> Insert size mean insert size = 1,633,145.8018 std insert size = 11,172,011.8317 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 39.2055 >>>>>>> ACTG content number of A's = 11,775,233 bp (28.55%) number of C's = 8,934,973 bp (21.67%) number of T's = 11,017,315 bp (26.72%) number of G's = 9,510,119 bp (23.06%) number of N's = 373 bp (0%) GC percentage = 44.73% >>>>>>> Mismatches and indels general error rate = 0.041 number of mismatches = 1,658,292 number of insertions = 25,533 mapped reads with insertion percentage = 7.15% number of deletions = 127,890 mapped reads with deletion percentage = 35.16% homopolymer indels = 27.44% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 3.2446X 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% 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 1456695 0.005844298377896519 3.12519201840884 chr2 243199373 1685343 0.00692988217531301 2.6201579141071427 chr3 198022430 809438 0.004087607651315056 1.556518449896948 chr4 191154276 1314869 0.006878574874254971 2.1588501249145566 chr5 180915260 1161896 0.006422321699120351 2.9962598560622338 chr6 171115067 1248182 0.007294401491833562 2.656583851938961 chr7 159138663 1514491 0.009516801080577132 2.906711503445182 chr8 146364022 595295 0.004067222203008332 1.1461139117928767 chr9 141213431 979636 0.0069372721352546135 2.7007053323659385 chr10 135534747 404581 0.002985072160130273 0.8531955664760396 chr11 135006516 1634904 0.012109815499571887 3.305378807959071 chr12 133851895 1153929 0.00862093883691374 2.748998800953651 chr13 115169878 587517 0.005101307826339801 1.702841324255809 chr14 107349540 190788 0.0017772595951505708 0.6771248043450075 chr15 102531392 470067 0.00458461541222419 1.3427989658048174 chr16 90354753 233810 0.002587688995176601 1.1277595732992238 chr17 81195210 590332 0.007270527411653963 2.670389829942586 chr18 78077248 303734 0.003890172973309715 1.4632380039219233 chr19 59128983 105827 0.001789765266214709 0.6524576652175385 chr20 63025520 312476 0.004957928153547959 1.5879612706208377 chr21 48129895 71286 0.0014811168817218487 0.3683525207913248 chr22 51304566 39086 7.618425229442541E-4 0.22198536437165692 chrMT 16571 12853 0.7756321284171143 4.742621650052594 chrX 155270560 24660794 0.15882466064397527 10.492373359474596 chrY 59373566 730772 0.012308036205876534 2.6327077093057434