BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094072.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 = 387,272 number of mapped reads = 374,102 (96.6%) number of supplementary alignments = 13,017 (3.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 187,979 number of mapped paired reads (second in pair) = 186,123 number of mapped paired reads (both in pair) = 371,574 number of mapped paired reads (singletons) = 2,528 number of mapped bases = 49,417,611 bp number of sequenced bases = 48,301,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 355,325 duplication rate = 50.95% >>>>>>> Insert size mean insert size = 519,365.8878 std insert size = 6,648,849.4535 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 39.2234 >>>>>>> ACTG content number of A's = 12,825,062 bp (26.55%) number of C's = 11,365,310 bp (23.53%) number of T's = 12,280,490 bp (25.42%) number of G's = 11,829,861 bp (24.49%) number of N's = 528 bp (0%) GC percentage = 48.02% >>>>>>> Mismatches and indels general error rate = 0.0412 number of mismatches = 1,912,346 number of insertions = 31,871 mapped reads with insertion percentage = 8.3% number of deletions = 150,323 mapped reads with deletion percentage = 38.22% homopolymer indels = 28.05% >>>>>>> Coverage mean coverageData = 0.016X std coverageData = 4.0511X There is a 0.01% 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% 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 432211 0.001734041818094407 0.6950999176253948 chr2 243199373 2183937 0.008980027263474894 3.5585809887069577 chr3 198022430 1171904 0.005918036658776483 2.2087943448904936 chr4 191154276 1098989 0.005749225301138437 1.8937896269566326 chr5 180915260 334278 0.0018477048315327298 0.7155725379501396 chr6 171115067 1268762 0.0074146714386056954 3.6121129769841165 chr7 159138663 1731458 0.010880184408737932 3.7768287583196103 chr8 146364022 1062519 0.007259427456837719 2.5978310582893753 chr9 141213431 650549 0.004606849330075409 1.982086896094679 chr10 135534747 915264 0.006752984162799226 2.1702208108408527 chr11 135006516 1913226 0.014171360440113868 4.012680157712016 chr12 133851895 1817065 0.013575190698644947 4.22717441815647 chr13 115169878 900389 0.007817920932416027 2.5552479151479837 chr14 107349540 377408 0.003515692754715111 1.4871822466180429 chr15 102531392 850320 0.00829326495440538 2.5904326486967664 chr16 90354753 305947 0.0033860642616111184 1.1356863491472138 chr17 81195210 1486262 0.018304799014621675 5.593020059761673 chr18 78077248 115792 0.0014830440745042654 0.48464838313067604 chr19 59128983 172833 0.0029229827950871404 0.7357566037649216 chr20 63025520 267382 0.0042424402051740315 1.104075027456673 chr21 48129895 605128 0.012572809477352901 5.369422179996108 chr22 51304566 88259 0.0017202952267445358 0.43851057011344446 chrMT 16571 1510574 91.15768511254602 415.08632722241316 chrX 155270560 27763520 0.17880736695996974 12.835757445549103 chrY 59373566 393635 0.006629802225455011 1.7109608958654998