TB-Profiler result

Run: ERR4872038
Summary

Run ID: ERR4872038

Sample name:

Date: 01-04-2023 21:19:10

Number of reads: 5183416

Percentage reads mapped: 99.74

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 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 0.2 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
ethA 4327384 c.89delA frameshift_variant 1.0 ethionamide, ethionamide
gid 4408100 c.102delG frameshift_variant 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
mshA 576108 p.Ala254Gly missense_variant 0.19
rpoB 761811 p.Phe669Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpR5 779121 c.138_139dupTG frameshift_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ald 3086896 c.79dupA frameshift_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.78
rpoA 3878613 c.-106A>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.99
embB 4246584 p.Arg24Pro missense_variant 0.3
embB 4249732 c.3219C>G synonymous_variant 1.0
whiB6 4338335 p.Ala63Thr missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0