WikiSysop: Created page with "'''Q1''' the read length is about 100bp but the actual insert size is unknown. '''Q2''' very low, less than 1% '''Q3''' About 40bp. '''Q4''' About 25%. '''Q5''' As and Gs '''Q6''' The sample indeed looks ancient. If we did not see DNA fragmentation or damage it could be indicative of present-day human contamination. '''Q7'''

 wc -l world.fam wc -l world.bim

297 samples and 587772 SNPs. '''Q8'''

 cut -f2 world.sampleInfo.txt | tail -n +2..."

2024-03-19T15:36:27Z

Created page with "'''Q1''' the read length is about 100bp but the actual insert size is unknown. '''Q2''' very low, less than 1% '''Q3''' About 40bp. '''Q4''' About 25%. '''Q5''' As and Gs '''Q6''' The sample indeed looks ancient. If we did not see DNA fragmentation or damage it could be indicative of present-day human contamination. '''Q7''' <pre> wc -l world.fam wc -l world.bim </pre> 297 samples and 587772 SNPs. '''Q8''' <pre> cut -f2 world.sampleInfo.txt | tail -n +2..."

New page

'''Q1'''

the read length is about 100bp but the actual insert size is unknown.

'''Q2'''

very low, less than 1%

'''Q3'''

About 40bp.

'''Q4'''

About 25%.

'''Q5'''

As and Gs

'''Q6'''

The sample indeed looks ancient. If we did not see DNA fragmentation or damage it could be indicative of present-day human contamination.

'''Q7'''

<pre>
wc -l world.fam
wc -l world.bim
</pre>
297 samples and 587772 SNPs.

'''Q8'''

<pre>
cut -f2 world.sampleInfo.txt | tail -n +2 | sort | uniq -c|sort -rn
70 Yoruba
33 Han
29 Basque
27 Sardinian
25 French
20 Hungarian
20 Greek
19 Bedouin2
17 Adygei
10 Lithuanian
10 Armenian
8 Tuscan
1 UstIshim
1 Stuttgart
1 Samara
1 NE1
1 MA1
1 Loschbour
1 Karelia
1 Iceman
1 Brana
</pre>

'''Q9:'''

You should be getting the same:
<pre>
plink --bfile world --missing --out world
587772 variants loaded from .bim file.
297 people (0 males, 0 females, 297 ambiguous) loaded from .fam.
</pre>

'''Q10:'''

<pre>
cat world.imiss |grep -i ice
Iceman Iceman Y 11873 587772 0.0202
</pre>

so about 2%.

'''Q11'''

<pre>
zcat RISE507.pileup.gz |wc -l
102014
</pre>

'''Q12'''

Using:
<pre>
plink --bfile world --bmerge RISE507 --out RISE507.merge
</pre>

should result in:
<pre>
Error: 253 variants with 3+ alleles present.
</pre>

This normally is due to tri-allelic sites. Normally they should be very few. However, in our case, there are a lot. This is likely due to damage that creates spurious variations.

'''Q13:'''

The Yoruba.

'''Q14:'''

The Han.

'''Q15:'''

The [https://en.wikipedia.org/wiki/Adyghe_people Adygei]

'''Q16'''

The Sardinians

'''Q17'''

the [https://en.wikipedia.org/wiki/Ust%27-Ishim_man Ust-Ishim] and the [https://en.wikipedia.org/wiki/Mal%27ta%E2%80%93Buret%27_culture Mal'ta–Buret' boy] (MA1).

There are many reasons that can explain this:
# the ancient individuals completely fall outside the range of genomic diversity of modern humans i.e. they were isolated populations that potentially died off.
# these were individuals with mixed ancestry
# they contain numerous errors due to damage

'''Q18:'''

The RISE507 sample from Afanasievo culture.

'''Q19:'''

Our individual is now a bit outside of the Hungarian / French cluster.

'''Q20'''

[https://www.nature.com/articles/nature14507 Allentoft et al. 2015] actually found that the individuals from the [https://en.wikipedia.org/wiki/Afanasievo_culture Afanasievo] were genetically indistinguishable from the [https://en.wikipedia.org/wiki/Yamnaya_culture Yamnhaya culture] which is a culture closely related to [https://en.wikipedia.org/wiki/Western_Steppe_Herders Western Steppe Herders] which is one of the major genetic contributor to present-day Europeans.

Ancient DNA exercise answers - Revision history