Open Access Research article

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

Judson A Ward1*, Jasbir Bhangoo2, Felicidad Fernández-Fernández3, Patrick Moore4, JD Swanson5, Roberto Viola6, Riccardo Velasco6, Nahla Bassil7, Courtney A Weber1 and Daniel J Sargent6

Author Affiliations

1 Department of Horticulture, Cornell University, New York State Agricultural Experiment Station, Geneva, New York, 14456, USA

2 Sector 18, Chandigarh, UT, 160018, India

3 East Malling Research (EMR), New Road, East Malling, Kent, ME, 19 6BJ, UK

4 Department of Horticulture and Landscape Architecture, Washington State University Puyallup Research and Extension Center, Puyallup, WA, 98372, USA

5 Department of Biology and Biomedical Sciences, Salve Regina University, 100 Ochre Point Ave, Newport, RI, 02840, USA

6 IASMA Research and Innovation Centre, Foundation Edmund Mach, Via E Mach 1, San Michele all’Adige, (TN), 38010, Italy

7 USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Rd, Corvallis, OR, 97333, USA

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BMC Genomics 2013, 14:2  doi:10.1186/1471-2164-14-2

Published: 16 January 2013

Additional files

Additional file 1: Figure S1:

The per base phred scores for Library One and Library Two showing the mean phred score (the point) and the upper and lower quartiles (the ends of lines).

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Additional file 2: Figure S2:

The per read phred scores and their frequencies for Library One and Library Two.

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Additional file 3: Figure S3:

The number of sequencing reads versus the number of unique sequencing reads for Library One and Library Two.

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Additional file 4: Table S1:

The count of over-represented sequencing reads, their position of alignment against the Fragaria vesca chloroplast genome (GenBank: JF345175.1), and the position of SNPs between the chloroplast sequences. (XLSX 53 kb)

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Additional file 5: Figure S4:

Percent missing values as a function of the number of sequencing reads per genotype.

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Additional file 6: Table S2:

The markers mapped to the two parental linkage maps of the H×T mapping progeny, including the linkage group and map position to which they were located, the SNP type and the nucleotide sequence flanking each side of each SNP.

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Additional file 7: Text S1:

The manual and additional descriptions of the imputation algorithm (Maskov).

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