provac-candidates outputs

Phylogeny used for calculating convergence scores (LCR)

Nextstrain tree of sequences from last ~6m

Salient-lineage reference tree

LCR comparisons between datasets

Per-root outputs

LF.7_matched

LCR tree
LF.7_desc
DMS root virus
KP.3.1.1
DMS data source
https://dms-vep.org/SARS-CoV-2_KP.3.1.1_spike_DMS
Root sequence
../data/sequences/lf7_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, L212I, usually because UShER cannot see indels. These positions are not shown in the LCR results or sequence-combination analysis.

Reversions (to any ancestral lineage) are excluded from every plot and statistic on this root.

XFG_matched

LCR tree
LF.7_desc
DMS root virus
KP.3.1.1
DMS data source
https://dms-vep.org/SARS-CoV-2_KP.3.1.1_spike_DMS
Root sequence
../data/sequences/xfg_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, L212I, usually because UShER cannot see indels. These positions are not shown in the LCR results or sequence-combination analysis.

Reversions (to any ancestral lineage) are excluded from every plot and statistic on this root.

PY.1_matched

LCR tree
LF.7_desc
DMS root virus
KP.3.1.1
DMS data source
https://dms-vep.org/SARS-CoV-2_KP.3.1.1_spike_DMS
Root sequence
../data/sequences/py1_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, L212I, usually because UShER cannot see indels. These positions are not shown in the LCR results or sequence-combination analysis.

Reversions (to any ancestral lineage) are excluded from every plot and statistic on this root.

RF_matched

LCR tree
LF.7_desc
DMS root virus
KP.3.1.1
DMS data source
https://dms-vep.org/SARS-CoV-2_KP.3.1.1_spike_DMS
Root sequence
../data/sequences/rf_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, L212I, usually because UShER cannot see indels. These positions are not shown in the LCR results or sequence-combination analysis.

Reversions (to any ancestral lineage) are excluded from every plot and statistic on this root.

XFJ_matched

LCR tree
LF.7_desc
DMS root virus
KP.3.1.1
DMS data source
https://dms-vep.org/SARS-CoV-2_KP.3.1.1_spike_DMS
Root sequence
../data/sequences/xfj_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, L212I, usually because UShER cannot see indels. These positions are not shown in the LCR results or sequence-combination analysis.

Reversions (to any ancestral lineage) are excluded from every plot and statistic on this root.

RW.1.1_matched

LCR tree
LF.7_desc
DMS root virus
KP.3.1.1
DMS data source
https://dms-vep.org/SARS-CoV-2_KP.3.1.1_spike_DMS
Root sequence
../data/sequences/rw11_aa.fasta

The curated root sequence and the UShER founder disagree at I19V, A27S, G142D, L212I, usually because UShER cannot see indels. These positions are not shown in the LCR results or sequence-combination analysis.

Reversions (to any ancestral lineage) are excluded from every plot and statistic on this root.

NB.1.8.1_matched

LCR tree
NB.1.8.1
DMS root virus
KP.3.1.1
DMS data source
https://dms-vep.org/SARS-CoV-2_KP.3.1.1_spike_DMS
Root sequence
../data/sequences/nb181_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, L212I, usually because UShER cannot see indels. These positions are not shown in the LCR results or sequence-combination analysis.

Reversions (to any ancestral lineage) are excluded from every plot and statistic on this root.

BA.2

LCR tree
BA.2
DMS root virus
BA.2
DMS data source
https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.2_spike_DMS_sera_and_mAbs
Root sequence
../data/sequences/ba2_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, usually because UShER cannot see indels. These positions are not shown in the LCR results.

XBB.1.5

LCR tree
XBB.1.5
DMS root virus
XBB.1.5
DMS data source
https://dms-vep.org/SARS-CoV-2_XBB.1.5_spike_DMS_infant_sera
Root sequence
../data/sequences/xbb15_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, usually because UShER cannot see indels. These positions are not shown in the LCR results.

JN.1

LCR tree
JN.1_desc
DMS root virus
KP.3.1.1
DMS data source
https://dms-vep.org/SARS-CoV-2_KP.3.1.1_spike_DMS
Root sequence
../data/sequences/jn1_aa.fasta

The curated root sequence and the UShER founder disagree at A27S, G142D, L212I, usually because UShER cannot see indels. These positions are not shown in the LCR results.