TB-Profiler result

Run: ERR2653236
Summary

Run ID: ERR2653236

Sample name:

Date: 31-03-2023 22:44:41

Number of reads: 9500953

Percentage reads mapped: 98.33

Strain: lineage4.1.2

Drug-resistance: Pre-XDR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
gyrA 7582 p.Asp94Gly missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 0.99 ethambutol
embA 4243242 p.Asp4Asn missense_variant 0.99 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326771 c.702delC frameshift_variant 0.99 ethionamide, ethionamide
ethR 4327876 p.Phe110Leu missense_variant 0.98 ethionamide
gid 4407944 c.258_259insA frameshift_variant 0.99 streptomycin
pncA 2284377 c.207_*4303del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
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
fgd1 491591 p.Lys270Met missense_variant 0.99
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764782 c.1413C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472259 n.414C>T non_coding_transcript_exon_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168303 c.2310G>T synonymous_variant 1.0
PPE35 2169776 p.Phe279Leu missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289034 p.Pro70Thr missense_variant 0.56
kasA 2518076 c.-39C>T upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840263 c.1158C>T synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.99
whiB6 4338232 p.Ser97Phe missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0