COV Ancestral Sequence Reconstruction--test

Test

Data: COV19 (Human) Spike gene

Remove duplicate sequences and sequence with unambiguous characters (For AA mutation, n= 817)

Ancestal sequence Reconstruction

IQtree--> get the ancestral sequence for all of the internal node, and summarize the mutation with more node included

TreeTime (limited by the number of sequences)

Ancestral sequence estimation + Map the mutation to the tree annotated_tree nexus

summary statisticsThe TOTAL tree length is 1.593e-01 and 718 mutations were observed. Of these 718 mutations,

547 occur 1 times
54 occur 2 times
9 occur 3 times
2 occur 6 times
1 occur 24 times

The TERMINAL branch length is 1.059e-01 and 520 mutations were observed. Of these 520 mutations,

432 occur 1 times
27 occur 2 times
2 occur 3 times
2 occur 6 times
1 occur 16 times

Of the 3822 positions in the genome,

3187 were hit 0 times (expected 3167.41)
445 were hit 1 times (expected 595.03)
82 were hit 2 times (expected 55.89)
17 were hit 3 times (expected 3.50)
2 were hit 4 times (expected 0.16)
2 were hit 5 times (expected 0.01)
1 were hit 9 times (expected 0.00)
1 were hit 31 times (expected 0.00)

log-likelihood difference to Poisson distribution with same mean: -1.326e+02

The ten most homoplasic mutations are: mut multiplicity G1841A 24 G1841R 6 G3371K 6 C13T 3 C52T 3 C870T 3 G906T 3 C1623T 3 C1860T 3 C2367T 3 C2472T 3 G3371T 3 C13Y 2 C60T 2 C65T 2 C80T 2 C84T 2 C86T 2 C96Y 2 C145T 2 C149T 2 C210T 2 C227T 2 G268T 2 T458C 2 G542T 2 G663T 2 G773T 2 G922T 2 G925C 2

The ten most homoplasic mutation on terminal branches are: mut multiplicity G1841A 16 G1841R 6 G3371K 6 C52T 3 C870T 3 C13Y 2 C96Y 2 C210T 2 C227T 2 G906T 2 G922T 2 G925C 2 G1356T 2 A1493M 2 C1524Y 2 G1723T 2 G1864A 2 C2073T 2 C2076T 2 A2108G 2 C2147T 2 G2306T 2 C2367T 2 C2472Y 2 C2820T 2 G3366T 2 G3371T 2 C3444T 2 A3498G 2 G3573T 2

Map AA mutation (simply translate the nucleotide to Amino acid)

aa_annotated_tree nexus

summary statistics The TOTAL tree length is 1.593e-01 and 424 mutations were observed. Of these 424 mutations,

307 occur 1 times
36 occur 2 times
3 occur 3 times
2 occur 6 times
1 occur 24 times

The TERMINAL branch length is 1.059e-01 and 302 mutations were observed. Of these 302 mutations,

239 occur 1 times
16 occur 2 times
1 occur 3 times
2 occur 6 times
1 occur 16 times

Of the 1273 positions in the genome,

950 were hit 0 times (expected 912.38)
198 were hit 1 times (expected 303.89)
66 were hit 2 times (expected 50.61)
11 were hit 3 times (expected 5.62)
4 were hit 4 times (expected 0.47)
1 were hit 5 times (expected 0.03)
1 were hit 9 times (expected 0.00)
1 were hit 31 times (expected 0.00)

log-likelihood difference to Poisson distribution with same mean: -1.134e+02

The ten most homoplasic mutations are: mut multiplicity G614D 24 G614X 6 G1124X 6 L5F 3 L18F 3 G1124V 3 L5X 2 T22I 2 P26X 2 A27V 2 T29I 2 H49Y 2 S50L 2 L54F 2 T76I 2 V90F 2 M153T 2 M177I 2 G181V 2 W258L 2 E281X 2 V308L 2 E309Q 2 V367F 2 G476S 2 Q498X 2 A522S 2 A575S 2 E583X 2 V622I 2

The ten most homoplasic mutation on terminal branches are: mut multiplicity G614D 16 G614X 6 G1124X 6 L18F 3 L5X 2 P26X 2 T76I 2 M177I 2 E281X 2 V308L 2 E309Q 2 Q498X 2 A575S 2 E583X 2 V622I 2 T716I 2 G769V 2 G1124V 2 V1228L 2 P1263X 2

JianiC / betaCoV