PRACTICAL 3: Coalescent
Date: Tuesday, 18 NOVEMBER 2025
STUDENTS: Dharti Jadhav, Dajla Belhaj, John Polugari, Tejaswini Srinivas Reddy
Problem 3.6 How many SNPs do you observe between positions 5,189,001 and
5,190,000 of chromosome 19? How many would be expected? Is the
difference between observation and expectation significant?
Answer:

tabix chr19.mgp.vcf.gz 19:5189001-5190000 | wc -l
40
We observe 40 SNPs between the position 5,189,001 and 5,190,000 on chromosome 19.

echo “1617408/61431566” | bc -l
0.02632861418509174908
The expected SNPs , P=0.02632 and to get expected number in 1000bp window we
multiply 0.0263 x 1000 ≈ 26.32.
So, the expected SNPs in 1000bp is ≈ 26 SNPs.

ms 34 10000 -t 6 |grep '^s’|awk '{if($2>=40)s++;c++}END{print "P"s/c)'
P=0.0659
This is slightly above the conventional 0.05 threshold for statistical significance. The
observed value (40) is higher than expected (~26).
The difference between observed (40) and expected (~26) SNPs is not statistically
significant at 𝛼 = 0.05. But it suggests a possible elevation, just not strong enough to be
conclusive.