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We estimated the mutation density based on Greene et al. [20] to 1 mutation every 573 kb.
Numbers in brackets were obtained after normalising to the average 35% GC content for the B. rapa genome [ 29]. ** Mutation density based on estimated number of mutations per plant divided by the 500,000 kb genome.
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VPM peak density (4.4 ± 0.6 × 10/mm) matched the peak density based on anatomical assumptions (4.04 × 10/mm).
This mutation density is higher than those found by earlier studies based on TILLING [ 7, 35– 35].
The mutation densities of the Ye5 subfamily were 1.99% and 11.34% for the non-CpG and CpG nucleotides yielding age estimates based on the average mutation density of 13.27 and 12.60 million years old.
To further delineate mutation favoured loci, we defined regions of high mutation density by identifying overlapping 150 base pair fragments containing higher than expected mutation loads (minimum of six mutations per fragment, originating from three independent transformants).
Because it is well established that EMS mutagenesis induces G/C to A/T transitions, the most conservative estimation of mutation density would only consider such base changes to be induced mutations.
Because heterozygotes are detected with lower efficiency, estimating the mutation density under these conditions would require adjusting the number of bases effectively assayed to 62 bases instead of 100.
The effect of Alu density on mutation feature based classification (a binary variable) was analyzed using a logistic regression model.
Although the overall mutation density in the library and individual plants was determined by whole-genome re-sequencing analysis based on 12 mutants, all of mutation for the targeted genes used for indexed amplicon sequencing remained unknown in 1536 mutantsants.
Based on the screening of six genes located on different chromosomes, we calculated a mutation density of ~1 per 60 kb and a 97% probability of identifying a stop-codon mutation in a standard screen of 3072 M2 plants.
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