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ktmeaton / ncov-recombinant

Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
MIT License
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Immune Escape Ranking #227

Open ktmeaton opened 1 year ago

ktmeaton commented 1 year ago

v0.7.0 (2023-02-23)

lineage rbd_level immune_escape ace2_binding
XBL 7 0.9070 1.0124
XBB.1.5 7 0.9070 1.0124
XBB 7 0.9070 0.4069
XBN 7 0.9070 0.4069
XBB.1 7 0.9070 0.4069
XBK 6 0.8366 1.0428
XBF 6 0.8366 1.0428
XBD 5 0.6339 0.4677
XBH 5 0.6339 0.4677
XBP 5 0.6307 0.6640
XBM 4 0.6014 0.6697
XBE 4 0.6014 0.6697
XBG 4 0.6014 0.6697
XBJ 5 0.5925 1.0634
XBC.1 4 0.5283 0.7927
XAY.1 4 0.5283 0.6144
XAY.2 4 0.5283 0.6144
XAY 4 0.5283 0.6144
XAS 3 0.3863 0.5583
XAZ 3 0.3863 0.5583
XAN 3 0.3863 0.5583
XAJ 3 0.3863 0.5583
XAV 3 0.3434 0.4963
XBC.2 3 0.3263 0.6872
XBA 3 0.3155 0.2022
XAK 2 0.2769 1.3052
XAW 4 0.2120 1.0223
XC 2 0.1935 -2.6545
XD 1 0.1528 -0.0291
XJ 0 0.0168 0.0082
XAG 0 0.0021 0.0419
XH 0 0.0002 -0.0078
XB 1 NA NA
XS 1 NA NA
XF 1 NA NA
XA 1 NA NA
XP 1 NA NA
XK 0 -0.0001 0.1551
XAE 0 -0.0001 0.0660
XAM 0 -0.0001 0.0583
XL 0 -0.0001 0.0000
XAR 0 -0.0001 0.0000
XAT 0 -0.0001 0.0000
XE 0 -0.0001 0.0000
XW 0 -0.0001 0.0000
XAC 0 -0.0001 0.0000
XAH 0 -0.0001 0.0000
XAQ 0 -0.0001 0.0000
XZ 0 -0.0001 0.0000
XAP 0 -0.0001 0.0000
XR 0 -0.0001 0.0000
XM 0 -0.0001 0.0000
XY 0 -0.0001 0.0000
XQ 0 -0.0001 0.0000
XT 0 -0.0001 0.0000
XG 0 -0.0001 0.0000
XAL 0 -0.0001 0.0000
XAF 0 -0.0001 0.0000
XV 0 -0.0001 0.0000
XN 0 -0.0001 0.0000
XAU 0 -0.0001 -0.0173
XAA 0 -0.0001 -0.0173
XAB 0 -0.0001 -0.0173
XU 0 -0.0001 -0.0191
XAD 0 -0.0001 -0.0345

Command to generate the from the GISAID controls:

csvtk cut -t -f "lineage,rbd_level,immune_escape,ace2_binding" results/controls-gisaid/linelists/lineages.tsv \
  | csvtk sort -t -k "immune_escape:nr,ace2_binding:nr" \
  | csvtk uniq -t -f "lineage" \
  | csvtk round -t -f "immune_escape,ace2_binding" -n 4 \
  | csvtk csv2md -t
ktmeaton commented 1 year ago

v0.7.0 (2023-01-25)

lineage rbd_level immune_escape ace2_binding
XBL 7 0.9070 1.0124
XBB.1.5 7 0.9070 1.0124
XBB 7 0.9070 0.4069
XBB.1 7 0.9070 0.4069
XBF 6 0.8366 1.0428
XBK 6 0.8366 1.0428
XBD 5 0.6339 0.4677
XBH 5 0.6339 0.4677
XBM 4 0.6014 0.6697
XBG 4 0.6014 0.6697
XBE 4 0.6014 0.6697
XBJ 5 0.5925 1.0634
XBJ-like 4 0.5515 0.1235
XBC.1 4 0.5283 0.7927
XAY 4 0.5283 0.6144
XAY.2 4 0.5283 0.6144
XAY.1 4 0.5283 0.6144
XAN 3 0.3863 0.5583
XAS 3 0.3863 0.5583
XAZ 3 0.3863 0.5583
XAJ 3 0.3863 0.5583
XAV 3 0.3434 0.4963
XBC.2 3 0.3263 0.6872
XBA 3 0.3155 0.2022
XAK 2 0.2769 1.3052
XAW 4 0.2120 1.0223
XC 2 0.1935 -2.6545
XD 1 0.1528 -0.0291
XJ 0 0.0168 0.0082
XAG 0 0.0021 0.0419
XH 0 0.0002 -0.0078
XP 1 NA NA
XA 1 NA NA
XB 1 NA NA
XF 1 NA NA
XS 1 NA NA
XK 0 -0.0001 0.1551
XAE 0 -0.0001 0.0660
XAM 0 -0.0001 0.0583
XAL 0 -0.0001 0.0000
XAT 0 -0.0001 0.0000
XAH 0 -0.0001 0.0000
XAP 0 -0.0001 0.0000
XAF 0 -0.0001 0.0000
XY 0 -0.0001 0.0000
XZ 0 -0.0001 0.0000
XAR 0 -0.0001 0.0000
XV 0 -0.0001 0.0000
XR 0 -0.0001 0.0000
XM 0 -0.0001 0.0000
XAQ 0 -0.0001 0.0000
XG 0 -0.0001 0.0000
XQ 0 -0.0001 0.0000
XW 0 -0.0001 0.0000
XAC 0 -0.0001 0.0000
XE 0 -0.0001 0.0000
XN 0 -0.0001 0.0000
XL 0 -0.0001 0.0000
XT 0 -0.0001 0.0000
XAA 0 -0.0001 -0.0173
XAU 0 -0.0001 -0.0173
XAB 0 -0.0001 -0.0173
XU 0 -0.0001 -0.0191
XAD 0 -0.0001 -0.0345