TB-Profiler result

Run: SRR14802007
Summary

Run ID: SRR14802007

Sample name:

Date: 03-04-2023 12:11:23

Number of reads: 1345411

Percentage reads mapped: 99.53

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 0.98
mshA 576108 p.Ala254Gly missense_variant 0.16
mshA 576613 c.1266A>C synonymous_variant 0.45
mshA 576616 c.1269G>C synonymous_variant 0.31
mshA 576628 c.1281G>C synonymous_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoB 760958 c.1152G>A synonymous_variant 0.11
rpoC 764367 p.Gly333Ala missense_variant 0.19
rpoC 765150 p.Gly594Glu missense_variant 0.96
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
fabG1 1673553 p.Asp38Glu missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.18
pepQ 2860159 p.Ala87Gly missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.78
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.5
rpoA 3878597 c.-90G>C upstream_gene_variant 0.5
rpoA 3878600 c.-93G>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.5
clpC1 4039606 p.Glu367Gln missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.45
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243813 p.Arg194Gln missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0