TB-Profiler result

Run: SRR18715093
Summary

Run ID: SRR18715093

Sample name:

Date: 03-04-2023 20:18:41

Number of reads: 3887443

Percentage reads mapped: 99.54

Strain: lineage4.1

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
lineage4.1 Euro-American T;X;H 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
mshA 576108 p.Ala254Gly missense_variant 0.16
mshA 576456 p.Val370Gly missense_variant 0.21
rpoC 764367 p.Gly333Ala missense_variant 0.16
rpoC 764438 c.1069C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801019 p.Thr71Ala missense_variant 1.0
atpE 1461209 c.165C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.43
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878597 c.-90G>C upstream_gene_variant 0.21
rpoA 3878613 c.-106A>C upstream_gene_variant 0.2
rpoA 3878641 c.-134C>G upstream_gene_variant 0.7
embC 4240409 p.Pro183Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.27
embB 4246584 p.Arg24Pro missense_variant 0.11
embB 4247296 c.783G>A synonymous_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0