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Exact(10)
So, changing the minimum read percentage with non-reference nucleotide could be critical to control false positive predictions.
We found that the minimum read percentage with non-reference nucleotide needed to predict a mutation was 3 12 times the average non-reference nucleotide frequency.
We found that when the quality score was increased, the minimum read percentage with non-reference nucleotide had to be decreased to detect all six know mutations.
The number of unique mutants was counted by a custom Python script when the maximum read percentage with non-reference nucleotide was 5%, and minimum read percentage with non-reference nucleotide ranged from 0.135% to 0.37%.
We used high-throughput sequencing, combined with a two-dimensional pooling strategy, with either minimum read percentage with non-reference nucleotide or minimum variance multiplier as mutation prediction parameters, to detect genes related to abiotic and biotic stress resistances.
Under these parameters (sequence quality scores from 10 to 21, and minimum read percentage with non-reference nucleotide from 0.058% to 0.37%), a set of unique mutants was detected (Table 4).
Similar(50)
When all known mutations can be detected, we set the threshold for minimum and maximum read percentage with non-reference nucleotide to detect new mutations for single copy genes.
For mutations in the conserved region to be effectively detected, perhaps a higher sequencing depth/minimum read percentage with non-reference nucleotide coverage needs to be achieved.
The acceptable percentage of identity was set to be >70%, the minimum read length was >35 nucleotides and the e-value cut-off was <10-6.
A pool of the processed reads from both cDNA libraries (TV1 and TV6) were clustered using the MIRA v2.9.26x3 assembler with the " de novo, normal, EST, 454" parameters, specifying a minimum read length of 40 nt, a minimum sequence overlap of 40 nt, and a minimum percentage overlap identity of 80%.
The minimum read length was 45 bp with a minimum Sanger quality score of 35.
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