TB-Profiler result

Run: ERR552878
Summary

Run ID: ERR552878

Sample name:

Date: 18-08-2022 09:21:29

Number of reads: 381803

Percentage reads mapped: 99.76

Strain: lineage4.4.1.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Asp missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 6372 p.Thr378Asn missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490600 c.-183C>T upstream_gene_variant 0.15
rpoC 766467 p.Glu1033Ala missense_variant 1.0
mmpR5 779426 p.Met146Thr missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.3
embR 1417463 c.-116A>G upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472281 n.436T>C non_coding_transcript_exon_variant 0.09
rrl 1475904 n.2247G>A non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156326 c.-215C>T upstream_gene_variant 0.1
kasA 2518282 c.170_171dupCG frameshift_variant 0.14
kasA 2518496 c.382C>T synonymous_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
panD 4044059 p.Ala75Ser missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243467 p.Ile79Phe missense_variant 0.11
embB 4248644 p.Ala711Ser missense_variant 0.12
ethA 4327394 p.Cys27Phe missense_variant 0.15
ethR 4328156 p.Leu203Pro missense_variant 0.11