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The CLR values obtained for this interval (ΛCLR >300) are within the top 1% of CLR values along the entire region of the X-chromosome analyzed and are above the significance threshold of 72 that corresponds to the 95th quantile of the top CLR values of 100 simulated subgenomic regions of 5 Mb.
We used the 95th quantile of the distribution of top CLR values as our significance threshold.
Furthermore, the averages of estimated irinotecan CLR values with two different initial distributions were within three fold of the values from the original report (data not shown).
These four SNPs are located within the 40-kb-long fragment enriched for SNPs showing significant CLR values between positions 65,000 and 105,000.
In both cases, a single window carries the most significant signal from each test: a combined p value of 0.00036 for chr4:158Mb, and 0.000015 for chr10 22Mb, and corresponding CLR values of 47 and 62.
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For every one of the simulated datasets, we computed the CLR-test statistic in the same way as we did for the observed dataset and recorded the maximum CLR value.
The CLR value between genes A and B was calculated by the formula: A z 2 + B z 2 Az and Bz are the z-score based on of A's and B's MI score distribution respectively between gene A and gene B [ 67].
Using a threshold by which the top 1 % of XP-CLR values (9.49) were selected, a total of 472 20 kb-windows exceeded the cutoff value.
Moreover, average significant XP-CLR values (13.3) from our improvement scan were substantially lower than those observed for maize improvement (XP-CLR = 19.1) [ 15].
The regions with the XP-CLR values in the top 1% of the empirical distribution (XP-CLR > 282.3) were designated candidate sweeps.
As expected, regions both downstream and upstream of this gene showed no significant selection signal with XP-CLR values ranging from 0 to 3.1 which did not exceed the cutoff value (Fig. 6c).
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