TB-Profiler result

Run: SRR7592383
Summary

Run ID: SRR7592383

Sample name:

Date: 04-04-2023 19:51:10

Number of reads: 3522962

Percentage reads mapped: 99.58

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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288848 c.393dupC frameshift_variant 1.0 pyrazinamide, pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
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
rpoC 764724 p.Phe452Cys 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
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.98
PPE35 2169902 c.711G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.34
ald 3086787 c.-33A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.44
fbiD 3339746 p.Ala210Gly missense_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.37
clpC1 4039889 c.816G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248324 p.Ala604Gly missense_variant 0.23
embB 4249732 c.3219C>G synonymous_variant 1.0
ethR 4327826 p.Asn93Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407627 c.575delG frameshift_variant 1.0