SNPs & indels Schizophyllum commune

This description accompanies four files containing SNPs and indels found in two sets of isolates of Schizophyllum commune. This dataset was created for and used in Nieuwenhuis, Nieuwhof and Aanen (2013) ====================================================================================<br>Populations used<br>------------------------------------------------------------------------------------<br>** 'Three branches' population **<br>First group are described in more detail in Nieuwenhuis et al. 2013. From the area of Wageningen 59 S. commune fruiting bodies were sampled from three different branches. Some fruiting bodies were of the same clonal origin and effectively 14 different individuals were present in the sample. Additionally to the 59 samples, the reference genome 4.8A (derived from reference strain 4-40; Forget et al., 2002; Ohm et al., 2010) was used. The DNA used for sequencing was obtained by DNA isolations using Qiagen DNEasy Plant Mini on each sample separately. DNA concentration was estimated using nanodrop measurements, after which each sample was mixed in equal concentration. The pooled DNA was used for whole genome Illumina sequencing by ServiceXS, Leiden, the Netherlands. From the<br>------------------------------------------------------------------------------------<br>** 'Europe and America' population **<br>Similar to the above described pooled DNA population a second pool was Illumina sequenced in a separate lane using 23 different isolates as well as the reference 4.8A reference strain. Each strain is isolated from a separate substratum. Strains used:<br>Sc04 ?, Brazil<br>Sc05 Wageningen, the Netherlands<br>Sc06 Wageningen, the Netherlands<br>Sc07 Wageningen, the Netherlands<br>Sc08 Wageningen, the Netherlands<br>Sc09 Wageningen, the Netherlands<br>Sc10 Renkum, the Netherlands<br>Sc11 Bennekom, the Netherlands<br>Sc12 Renkum, the Netherlands<br>Sc13 Bennekom, the Netherlands<br>Sc15 ?, Germany<br>Sc16 La Palma, Canary Islands<br>Sc17 Utrecht - Uithof, the Netherlands<br>Sc18 Utrecht - St. Helena, the Netherlands<br>Sc19 Utrecht - Beaufort, the Netherlands<br>Sc20 Utrecht - Loenen, the Netherlands<br>Sc21 Utrecht - Barnsweert, the Netherlands<br>Sc22 Zeist, Zeisterbos, the Netherlands<br>Sc23 "Wilhelmina", the Netherlands<br>Sc27 Plitvica, Slovenia<br>Sc28 Bohinj, Slovenia<br>Sc29 ?, Denmark<br>Sc35 Kraków, Poland<br>4.8A Derived from reference strain 4-40 (Forget et al., 2002; Ohm et al., 2010) ====================================================================================<br>Description of files<br>------------------------------------------------------------------------------------<br>** snps_mtDNA_Schizophyllum_commune_3branches.csv **<br>Tab delimited file describing single nucleotide polymorphisms (SNP) relative to the reference mitochondrial genome of Schizophyllum commune as deposited in NCBI under gi|15077911 (or gb|AF402141.1). See the general description how these data were obtained above. Columns described in the file are:<br>- Reference_genome - reference to the NCBI reference sequence<br>- Position_in_reference_genome - position of snp relative to reference genome<br>- allele_reference - basepair at this position in the reference genome<br>- SNP - all alternative alleles at this position<br>- Var - mose observed alternative SNP at this position<br>- Freq - Frequency of this allele described at 'Var'<br>- Pval - probability the variation is an actual SNP<br>- depth - total number of reads at this position<br>- #A - number of reads containing basepair 'A'<br>- #C - number of reads containing basepair 'C'<br>- #G - number of reads containing basepair 'G'<br>- #T - number of reads containing basepair 'T'<br>------------------------------------------------------------------------------------<br>** indel_mtDNA_Schizophyllum_commune_3branches.txt **<br>Tab delimited file describing single nucleotide polymorphisms (SNP) relative to the reference mitochondrial genome of Schizophyllum commune as deposited in NCBI under gi|15077911 (or gb|AF402141.1). See the general description how these data were obtained above. Columns described in the file are:<br>- Reference_genome - reference to the NCBI reference sequence<br>- Position_in_reference_genome - position of snp relative to reference genome<br>- allele_reference - basepair at this position in the reference genome<br>- Variation_found - observed basepares that are inserted (+) or deleted (-) at the position<br>- Reads1 - number of reads of the reference genome allele<br>- Reads2 - number of reads of the indel type<br>- Freq - Frequency of the allele described at 'Variation_found'<br>- Pvalue - probability the variation is an actual SNP ------------------------------------------------------------------------------------<br>** snps_mtDNA_Schizophyllum_commune_euram.txt **<br>Tab delimited file describing single nucleotide polymorphisms (SNP) relative to the reference mitochondrial genome of Schizophyllum commune as deposited in NCBI under gi|15077911 (or gb|AF402141.1). Data obtained for the "'Europe and America' population". See the general description how these data were obtained above. Columns described in the file are:<br>- Reference_genome - reference to the NCBI reference sequence<br>- Position_in_reference_genome - position of snp relative to reference genome<br>- allele_reference - basepair at this position in the reference genome<br>- SNP - all alternative alleles at this position<br>- Var - mose observed alternative SNP at this position<br>- Freq - Frequency of this allele described at 'Var'<br>- Pval - probability the variation is an actual SNP<br>- depth - total number of reads at this position<br>- #A - number of reads containing basepair 'A'<br>- #C - number of reads containing basepair 'C'<br>- #G - number of reads containing basepair 'G'<br>- #T - number of reads containing basepair 'T'<br>------------------------------------------------------------------------------------<br>** indel_mtDNA_Schizophyllum_commune_euram.txt **<br>Tab delimited file describing indels relative to the reference mitochondrial genome of Schizophyllum commune as deposited in NCBI under gi|15077911 (or gb|AF402141.1). Data obtained for the "'Europe and America' population". See the general description how these data were obtained above. Columns described in the file are:<br>- Reference_genome - reference to the NCBI reference sequence<br>- Position_in_reference_genome - position of snp relative to reference genome<br>- allele_reference - basepair at this position in the reference genome<br>- Variation_found - observed basepares that are inserted (+) or deleted (-) at the position<br>- Reads1 - number of reads of the reference genome allele<br>- Reads2 - number of reads of the indel type<br>- Freq - Frequency of the allele described at 'Variation_found'<br>- Pvalue - probability the variation is an actual SNP