TB-Profiler result

Run: SRR15316364
Summary

Run ID: SRR15316364

Sample name:

Date: 03-04-2023 13:26:41

Number of reads: 6958315

Percentage reads mapped: 99.49

Strain: lineage4.4.2

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761078 p.Phe424Leu missense_variant 1.0 rifampicin
rpoB 761139 p.His445Tyr missense_variant 0.99 rifampicin
katG 2153980 c.2130_2131delCT frameshift_variant 0.99 isoniazid
ahpC 2726119 c.-74G>A upstream_gene_variant 0.99 isoniazid
embB 4247431 p.Met306Ile missense_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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761830 p.Gly675Asp 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
rpsA 1833627 p.Thr29Met missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917993 c.54A>G synonymous_variant 1.0
PPE35 2168774 c.1839G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289193 p.Gly17Cys missense_variant 1.0
pepQ 2859493 p.Gly309Glu missense_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
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
embB 4246508 c.-6G>A upstream_gene_variant 1.0
embB 4248004 p.Gln497His missense_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407916 p.Arg96Leu missense_variant 1.0
Rv2752c 3063325 c.357_*1189del frameshift_variant&stop_lost&splice_region_variant 1.0