PP_001105M.1

Display Name: Senegal/PP_001105M.1/2022-09-01
Sene, O.

Submission details

Submission ID
PP894723.1.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
99.66%
Frame shifts M
GPC:10-36(nt:118-200),GPC:39-43(nt:205-220),GPC:48-85(nt:234-346),GPC:99-127(nt:387-471),GPC:132-190(nt:484-662),GPC:200-222(nt:689-758),GPC:228-237(nt:772-803),GPC:240-332(nt:810-1088),GPC:338-1685(nt:1102-5147)
Length M
5368
Total ambiguous nucs M
0
Total deleted nucs M
155
Total frame shifts M
9
Total inserted nucs M
175
Total SNPs M
1333
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
PP894723.1
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:G50T
  • M:A51G
  • M:A52T
  • M:C63G
  • M:T65A
  • M:T67A
  • M:A69G
  • M:A70T
  • M:G84C
  • M:A90T
  • M:C96A
  • M:A99T
  • M:C103G
  • M:T105C
  • M:T109C
  • M:G110T
  • M:A112C
  • M:C120T
    • Deletions
    M:73-81, M:86, M:87, M:93, M:94, M:114-117, M:153-161, M:221-224, M:246-248, M:264-275, M:300-308, M:379-386, M:472, M:483, M:601-603, M:638-652, M:676-688, M:738-740, M:759, M:760, M:768-771, M:1095-1101, M:5146, M:5157-5164, M:5168-5192, M:5198, M:5199, M:5261-5264, M:5285, M:5286, M:5289, M:5334
    Insertions
    ins_M:662:A, ins_M:5246:C, ins_M:626:ACA, ins_M:59:TGT, ins_M:236:CCG, ins_M:200:TCTTCAA, ins_M:454:ACC, ins_M:233:CAGAAACA, ins_M:182:ACTAGCTC, ins_M:191:T, ins_M:803:ACTGCTATTG, ins_M:1088:ACCCAGA, ins_M:346:AGAA, ins_M:467:TTGGA, ins_M:204:TTCAAATAGTACAATGTCTGTG, ins_M:5294:CAATCAACTTTGC, ins_M:5209:AATATT, ins_M:5241:GC, ins_M:749:AAGATTCAA, ins_M:5225:ATACT, ins_M:5217:AT, ins_M:432:ACACCACAT, ins_M:5152:T, ins_M:408:AACCCAAGTACTACGGCTG, ins_M:809:TA, ins_M:101:TGTTGT, ins_M:403:TCAGGG, ins_M:55:TGAAAAGC, ins_M:5320:C

    Amino acid mutations

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

    Substitutions

    GPC

  • GPC:S86Y
  • GPC:S90L
  • GPC:G192Y
  • GPC:P193Q
  • GPC:T194P
  • GPC:E195K
  • GPC:P239S
    • Deletions
    GPC:44, GPC:97, GPC:98, GPC:131, GPC:196-199, GPC:223, GPC:226, GPC:227, GPC:335-337
    Insertions
    ins_GPC:52:PQK, ins_GPC:44:LQTLQIVQCL, ins_GPC:90:TPPSK

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