PP_001109D.1

Display Name: Senegal/PP_001109D.1/2022-09-01
Sene, O.

Submission details

Submission ID
PP894727.1.M
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-01-22 09:24:35 UTC
Date released
2025-01-22 09:25:07 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-01-22 09:24insdc_ingest_userOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
Institut Pasteur, Dakar, Virology

Alignment and QC metrics M

Completeness M
99.98%
Frame shifts M
GPC:8(nt:113-116),GPC:22-24(nt:154-163),GPC:35-36(nt:193-198),GPC:41-49(nt:211-239),GPC:58-60(nt:262-272),GPC:102-104(nt:394-404),GPC:123-131(nt:458-485),GPC:159-160(nt:566-572),GPC:203-205(nt:698-705),GPC:208-214(nt:713-732),GPC:222-226(nt:756-770),GPC:229-230(nt:777-782),GPC:239(nt:805-809),GPC:325-329(nt:1063-1079),GPC:385-386(nt:1244-1250)
Length M
5431
Total ambiguous nucs M
1
Total deleted nucs M
150
Total frame shifts M
15
Total inserted nucs M
215
Total SNPs M
1270
Total unknown nucs M
0

Sample details

Earliest release date
2025-01-18
Collection country
Senegal
Collection date
2022-09
Collection date (lower bound)
2022-09-01
Collection date (upper bound)
2022-09-30

Host

Host name scientific
Hyalomma impeltatum
Host taxon id
563069

INSDC

INSDC accession M
PP894727.1
NCBI release date
2025-01-18

Nucleotide mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

Substitutions

M

  • M:T40C
  • M:A51G
  • M:T58G
  • M:A61T
  • M:G62T
  • M:C77T
  • M:A78C
  • M:T79A
  • M:C82A
  • M:C85T
  • M:A87G
  • M:C89T
  • M:T94A
  • M:G95A
  • M:T98C
  • M:C103T
  • M:A107G
  • M:A108T
    • Deletions
    M:65-72, M:111, M:112, M:134-153, M:207-210, M:222, M:234-236, M:246-254, M:258-261, M:351-359, M:393, M:405, M:406, M:414-419, M:437-439, M:585-587, M:591-593, M:663-683, M:697, M:733-743, M:783, M:784, M:810, M:811, M:1059-1062, M:1083-1085, M:1240-1243, M:5158-5162, M:5193-5197, M:5208-5218, M:5293, M:5294, M:5335
    Insertions
    ins_M:371:AGC, ins_M:1079:C, ins_M:755:C, ins_M:479:GCA, ins_M:198:AC, ins_M:485:CAAACCCCAGAAGC, ins_M:5151:G, ins_M:284:CAT, ins_M:705:AAAGGGG, ins_M:185:TCCCAC, ins_M:172:CATCAGCCC, ins_M:689:TCCTTC, ins_M:5307:AGCGTATGTGA, ins_M:5231:TTCAC, ins_M:5251:GTATTAACAGTA, ins_M:301:CTCCGA, ins_M:770:TTCAGACT, ins_M:338:TCAGCC, ins_M:565:ACAGCTCG, ins_M:87:TGTC, ins_M:272:CGATAGATCA, ins_M:5224:GGGCTG, ins_M:5265:G, ins_M:239:CA, ins_M:51:TGCT, ins_M:116:TT, ins_M:5173:GCAACAGCAGCAAACCCCTTCCCCG, ins_M:1250:CATT, ins_M:572:G, ins_M:712:AA, ins_M:457:C, ins_M:776:CT, ins_M:163:GGAGCTTC, ins_M:1097:CACACA, ins_M:5323:TC, ins_M:5314:A, ins_M:804:TGGAGGCAATT, ins_M:192:TATC, ins_M:5182:TAAATCA

    Amino acid mutations

    Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

    Substitutions

    GPC

  • GPC:M1K
  • GPC:S4L
  • GPC:M6F
  • GPC:C11Y
  • GPC:L12H
  • GPC:T34I
  • GPC:L52T
  • GPC:V61T
  • GPC:T62P
  • GPC:T64H
  • GPC:S68T
  • GPC:G69P
  • GPC:L70I
  • GPC:E71S
  • GPC:P81A
  • GPC:I82T
  • GPC:L89A
  • GPC:E91A
    • Deletions
    GPC:7, GPC:15-21, GPC:25-31, GPC:39, GPC:40, GPC:56, GPC:57, GPC:76-78, GPC:84-87, GPC:101, GPC:105, GPC:108-111, GPC:154-158, GPC:161-164, GPC:202, GPC:215-217, GPC:231, GPC:240, GPC:323, GPC:324, GPC:384
    Insertions
    ins_GPC:94:SPEPTSAAQPSPT, ins_GPC:71:EA, ins_GPC:174:TIHTTKEATKAT, ins_GPC:19:SNTTISPT, ins_GPC:179:A, ins_GPC:238:EAI

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