TB-Profiler result

Run: SRR7341699

Summary

Run ID: SRR7341699

Sample name:

Date: 19-10-2023 19:07:18

Number of reads: 3976333

Percentage reads mapped: 99.69

Strain: lineage4.4.1.1

Drug-resistance: MDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Met434Leu (1.00), rpoB p.His445Asn (1.00), rpoB p.Pro454Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Leu (1.00)
Pyrazinamide R pncA p.Gly17Asp (1.00)
Streptomycin R gid p.Ser136* (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
rpoB 761106 p.Met434Leu missense_variant 1.0 rifampicin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
rpoB 761167 p.Pro454Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289192 p.Gly17Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
gid 4407796 p.Ser136* stop_gained 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619785 c.-106G>C upstream_gene_variant 1.0
mmpL5 775626 p.Trp952Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086868 c.51_54dupCATC frameshift_variant 0.57
ald 3087718 p.Asn300Thr missense_variant 0.36
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
alr 3841608 c.-188A>G upstream_gene_variant 1.0
clpC1 4040522 c.183T>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268041 c.796C>T synonymous_variant 1.0
ubiA 4269671 p.Val55Leu missense_variant 1.0
ethA 4326019 c.1455C>T synonymous_variant 1.0
ethA 4326267 p.Cys403Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0