Sample informations

In this section we explore the characteristics of the samples that we have sequenced: geographical origin, type, date of sampling …

Sampling characteristics

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Overall sequencing stats

Plot quality checks of the sequencing outcome.

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Overall LoFreq Stats

Number and type of variants per sample correlated with sample characteristics (gender, Ct values, sequencing quality …).

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gene typeVar number length density
19 ORF1AB missense_variant 3809 21290 0.1789103
20 ORF1AB indel 2622 21290 0.1231564
17 ORF1AB synonymous_variant 1343 21290 0.0630813
18 ORF1AB other 249 21290 0.0116956
41 S missense_variant 580 3822 0.1517530
42 S indel 406 3822 0.1062271
43 S synonymous_variant 174 3822 0.0455259
44 S other 50 3822 0.0130822
24 ORF3A missense_variant 132 828 0.1594203
21 ORF3A indel 96 828 0.1159420
22 ORF3A synonymous_variant 46 828 0.0555556
23 ORF3A other 7 828 0.0084541
2 E missense_variant 30 228 0.1315789
3 E indel 25 228 0.1096491
4 E synonymous_variant 7 228 0.0307018
1 E other 5 228 0.0219298
7 M missense_variant 101 669 0.1509716
8 M indel 83 669 0.1240658
5 M synonymous_variant 47 669 0.0702541
6 M other 6 669 0.0089686
25 ORF6 missense_variant 22 186 0.1182796
26 ORF6 indel 19 186 0.1021505
27 ORF6 synonymous_variant 8 186 0.0430108
28 ORF6 other 4 186 0.0215054
30 ORF7A missense_variant 46 366 0.1256831
31 ORF7A indel 42 366 0.1147541
32 ORF7A synonymous_variant 26 366 0.0710383
29 ORF7A other 12 366 0.0327869
35 ORF7B missense_variant 22 132 0.1666667
36 ORF7B indel 21 132 0.1590909
33 ORF7B synonymous_variant 6 132 0.0454545
34 ORF7B other 1 132 0.0075758
40 ORF8 missense_variant 58 366 0.1584699
37 ORF8 indel 35 366 0.0956284
38 ORF8 synonymous_variant 20 366 0.0546448
39 ORF8 other 4 366 0.0109290
9 N missense_variant 212 1260 0.1682540
10 N indel 135 1260 0.1071429
11 N synonymous_variant 78 1260 0.0619048
12 N other 23 1260 0.0182540
14 ORF10 missense_variant 28 117 0.2393162
15 ORF10 indel 13 117 0.1111111
16 ORF10 synonymous_variant 10 117 0.0854701
13 ORF10 other 2 117 0.0170940 

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variable value
nbrVariants_2 23
nbrVariants_2_50 15 
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Per position graphs

Variant distribution across the genome and frequency classes.

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Var1 Freq
1 6304
2 1665
3 541
4 199
5 108
6 58
7 33
8 23
10 16
11 13
9 11
13 8
15 8
12 4
16 3
18 3
21 3
143 3
14 2
17 2
33 2
371 2
19 1
20 1
23 1
27 1
30 1
36 1
39 1
40 1
41 1
44 1
58 1
67 1
86 1
98 1
315 1
334 1
372 1
386 1

Figure 2B and 2D (towards fixation: Tyrol1 and Vienna1)

Highlight positions Vienna1

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Highlight positions Ischgl

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Figure 3B and S6G (Bottleneck)

The distribution of bottleneck sizes with different cutoffs across the infector-infectee pairs.

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Clinical info bottleneck samples

Number of variants and Ct values for each sample in the pairs used for bottleneck estimates.

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Compare the bottleneck values

Compare the bottleneck estimates between the different cutoffs.

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Make the TV plots

Plot the comparison of variants and their respective frequencies in the samples of each infector-infectee pair used for the bottleneck size computation.

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Patient samples

Plot the variants and their frequency evolution in patients with minimum 2 independent samples available.

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Variants shared between pairs of samples

Make pairs of unrelated samples in order to compare the sharing of variants intra-patient with random sharing of variants.

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