TB-Profiler result

Run: ERR4827473
Summary

Run ID: ERR4827473

Sample name:

Date: 01-04-2023 18:05:38

Number of reads: 1413521

Percentage reads mapped: 99.43

Strain: lineage4.2.1

Drug-resistance: HR-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
lineage4.2.1 Euro-American (TUR) H3;H4 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
katG 2155647 p.Tyr155* stop_gained 1.0 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
gid 4408087 c.115delC 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8742 p.Asp481His missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303876 p.Ala316Thr missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155307 p.Gly269Ser missense_variant 0.13
PPE35 2167814 c.2799C>T synonymous_variant 0.13
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.42
PPE35 2170053 p.Thr187Ser missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289875 c.-634C>T upstream_gene_variant 0.11
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449192 p.Leu230Gln missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246266 p.Lys1012Glu missense_variant 0.1
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.12
embB 4246567 c.54G>T synonymous_variant 0.12
embB 4249459 c.2946G>A synonymous_variant 0.12
embB 4249594 c.3081G>A synonymous_variant 1.0
embB 4249671 p.Leu1053Gln missense_variant 0.22
aftB 4268877 c.-41T>C upstream_gene_variant 0.11
ubiA 4269111 p.Asp241Glu missense_variant 0.12
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0