BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094047.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 = 471,330 number of mapped reads = 440,186 (93.39%) number of supplementary alignments = 15,403 (3.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 221,061 number of mapped paired reads (second in pair) = 219,125 number of mapped paired reads (both in pair) = 436,950 number of mapped paired reads (singletons) = 3,236 number of mapped bases = 57,291,345 bp number of sequenced bases = 55,723,413 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 416,965 duplication rate = 50.37% >>>>>>> Insert size mean insert size = 402,099.5639 std insert size = 5,494,323.7171 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 42.2292 >>>>>>> ACTG content number of A's = 15,655,239 bp (28.09%) number of C's = 12,287,109 bp (22.05%) number of T's = 14,962,855 bp (26.85%) number of G's = 12,817,645 bp (23%) number of N's = 565 bp (0%) GC percentage = 45.05% >>>>>>> Mismatches and indels general error rate = 0.047 number of mismatches = 2,548,814 number of insertions = 41,686 mapped reads with insertion percentage = 9.33% number of deletions = 205,104 mapped reads with deletion percentage = 43.52% homopolymer indels = 29.03% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 4.507X 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% 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 1095870 0.004396659055866505 1.9046519985350527 chr2 243199373 2248179 0.009244180905022317 2.776357032676239 chr3 198022430 1479079 0.007469249821850989 2.3951574940063316 chr4 191154276 1529198 0.00799981058231729 2.2054967461731034 chr5 180915260 597047 0.0033001472623149647 1.372001237022507 chr6 171115067 1779134 0.010397295990305751 5.438032044680415 chr7 159138663 2157182 0.01355536083648007 4.013396642421871 chr8 146364022 1041639 0.007116769447617393 2.0640331797062004 chr9 141213431 1030851 0.007299950101771835 2.887934431813595 chr10 135534747 2094804 0.015455844691988838 4.878314989003192 chr11 135006516 2278372 0.016876015080635073 4.428282291145038 chr12 133851895 2159099 0.016130507528488856 4.226308513609294 chr13 115169878 1548589 0.013446128683057213 3.399287152720965 chr14 107349540 367358 0.0034220733502910213 1.2053028799322638 chr15 102531392 894638 0.008725503307318796 2.3963952985460937 chr16 90354753 507589 0.005617734354273538 1.9347053579828621 chr17 81195210 1028858 0.012671412513127313 3.159842406127504 chr18 78077248 282079 0.0036128194477346334 0.8790741121456623 chr19 59128983 359985 0.006088131094695135 1.6984600884572434 chr20 63025520 413342 0.006558327483850986 2.031587840568265 chr21 48129895 335210 0.006964694188507995 1.9288274304228188 chr22 51304566 215397 0.004198398247828468 1.1701550193931465 chrMT 16571 2305623 139.13602075915756 568.789609505486 chrX 155270560 29166979 0.18784616349680197 13.927358748915523 chrY 59373566 375244 0.006320051586593266 2.0116599683132503