TB-Profiler result

Run: SRR13583416
Summary

Run ID: SRR13583416

Sample name:

Date: 03-04-2023 08:59:59

Number of reads: 949154

Percentage reads mapped: 83.47

Strain: lineage4.7

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
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326699 c.774delG frameshift_variant 1.0 ethionamide, ethionamide
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
rpoB 763017 p.Gln1071Glu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304992 p.Ser688Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
rrl 1476415 n.2758C>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073972 p.Ser167Asn missense_variant 0.17
thyA 3074348 p.Phe42Ile missense_variant 1.0
clpC1 4040605 p.Leu34Ile missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embB 4249732 c.3219C>G synonymous_variant 1.0
aftB 4267191 p.Gly549Asp missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0