This is a demo instance. You can upload any data you like, including test data to try things out. You can find test data to upload in the example data repository. This instance should not be used for analysis.

PPD_00483VL.1

Display Name: Senegal/PPD_00483VL.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 09:27:21 UTC
Date released
2025-01-22 09:27:44 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-01-22 09:27insdc_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

    Report an issue with this sequence or metadata

    Create GitHub issue