TB-Profiler result

Run: SRR8380892
Summary

Run ID: SRR8380892

Sample name:

Date: 20-10-2023 21:26:35

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
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
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
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
gyrB 5965 c.726A>G synonymous_variant 0.98
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9328 p.Ala676Val missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
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 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726103 c.-90G>A upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyA 3074141 p.Gln111* stop_gained 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338286 c.235delG frameshift_variant 1.0
whiB6 4338513 c.9C>T synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
ethA 4326351 c.736_1122del conservative_inframe_deletion 1.0