daphmag15nwblg2r --------------------------------------- This uses published DNA and scaffolds of daphmag_2010nwb, and linkage map data from these two sources for this genome assembly: Duki, M., Berner, D., Roesti, M. et al. A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna . BMC Genet 17, 137 (2016). https://doi.org/10.1186/s12863-016-0445-7 Routtu et al. An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits BMC Genomics 2014, 15:1033. http://www.biomedcentral.com/1471-2164/15/1033 Chromosome scaffolds are placed in the 10 linkage groups identified with this data, using http://catchenlab.life.illinois.edu/chromonomer/ software. Linkage groups and Mbase size are DC01 13.5, DC02 16.1, DC03 9.4, DC04 9.1, DC05 8.5, DC06 9.3, DC07 9.5, DC08 9.4, DC09 7.2, DC10 9.9, This table dmag15nwblg2r_chrs.agp maps scaffolds onto DC chromosomes. Some 20 Mb of unplaced scaffolds are including as well. These sequences are in dmag15nwblg2r_all.fa.gz, with dmag15nwblg2r_all.facount tabulating chromosme + unplaced scaffold sizes. daphmag_2010nwb --------------------------------------- assembed size: 134 Mb, est. size 227 Mb with unassembled reads 41303 scaffolds total, largest 2.8 Mb Published to NCBI GenBank stats for nwbdmag24g7d: Roche Solexa gDNA paired reads, Newbler 2013 assembler read sizes ~700bp, pair insert sizes 500 to 20,000bp 13x coverage peakDepth, 3405 scaffolds, N50=545719, estimatedGenomeSize = 227.0 MB (Newbler software est.) 64% of reads assembled Unassembled 36% reads: Repeats= 3332814, 21.22%; << meaningful, missing chr parts Singletons = 1736006, 11.05%; << missing chromosome parts Partial = 562419, 3.58% Unassembled gDNA reads mapped to chrasm and trasm: transcript set: dmagset7finloc9b.gff exons nx=176534; exonw=303.7; sw=53630391; =~ 46% of chrasm NCBI Report # Assembly Statistics Report # Assembly name: daphmag2.4 # Organism name: Daphnia magna (crustaceans) # Infraspecific name: strain=Xinb3 # Sex: pooled male and female # Taxid: 35525 # BioSample: SAMN03703141 # BioProject: PRJNA298946 # Submitter: Indiana University # Date: 2016-04-26 # Assembly type: haploid # Release type: major # Assembly level: Scaffold # Genome representation: full # WGS project: LRGB01 # Assembly method: Newbler v. 2.3 091027_1459 # Expected final version: no # Genome coverage: 13.0x # Sequencing technology: 454 # GenBank assembly accession: GCA_001632505.1 # # Assembly-Units: # GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name # GCA_001632515.1 Primary Assembly ---------------------------------------