TB-Profiler result

Run: ERR4799163
Summary

Run ID: ERR4799163

Sample name:

Date: 01-04-2023 08:55:13

Number of reads: 5676793

Percentage reads mapped: 99.51

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 0.98
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.98
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.98
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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155289 p.Thr275Ala missense_variant 0.97 isoniazid
pncA 2289015 p.Thr76Ile missense_variant 0.98 pyrazinamide
eis 2715342 c.-10G>C upstream_gene_variant 0.99 kanamycin, kanamycin
embB 4248025 p.Glu504Asp missense_variant 0.99 ethambutol
ethA 4326118 c.1355delG frameshift_variant 0.98 ethionamide
gid 4408100 c.102delG frameshift_variant 0.99 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
gyrB 5965 c.726A>G synonymous_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9328 p.Ala676Val missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.99
rpoB 761489 c.1683G>A synonymous_variant 0.97
rpoC 764936 p.Gln523Glu missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305180 c.2250G>A synonymous_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.95
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.99
thyA 3074077 p.Ala132Val missense_variant 0.99
ald 3086742 c.-78A>C upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448664 p.Arg54His missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 0.96
whiB6 4338513 c.9C>T synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0