TB-Profiler result

Run: SRR12708377
Summary

Run ID: SRR12708377

Sample name:

Date: 02-08-2023 14:45:30

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 0.9
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.91
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 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288953 p.Gly97Cys missense_variant 0.81 pyrazinamide
gid 4407830 p.Gln125* stop_gained 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 5778 p.Phe180Cys missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.9
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407243 p.Leu33Arg missense_variant 0.5
embR 1417116 p.Asn78His missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674797 p.Met199Arg missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170432 p.Ser61Ala missense_variant 0.18
Rv1979c 2223051 p.Glu38Asp missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 1.0
thyX 3067416 p.Asn177Thr missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612997 c.120T>G synonymous_variant 0.2
fbiA 3641447 p.Thr302Met missense_variant 0.92
alr 3840807 p.Asp205Ala missense_variant 0.29
rpoA 3877553 p.Glu319Lys missense_variant 0.93
embC 4240170 p.Thr103Met missense_variant 0.22
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4240907 p.Leu349Met missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.75
embB 4249408 c.2895G>A synonymous_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0