TB-Profiler result

Run: SRR14165028
Summary

Run ID: SRR14165028

Sample name:

Date: 03-04-2023 10:13:10

Number of reads: 4734528

Percentage reads mapped: 99.69

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 0.98
lineage4.4.1.1 Euro-American S;Orphans None 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
ahpC 2726119 c.-74G>A upstream_gene_variant 0.99 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 0.18
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 1673380 c.-60C>G upstream_gene_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.28
PPE35 2170053 p.Thr187Ser missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.16
thyA 3073880 p.Glu198Lys missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.35
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.99
rpoA 3877919 p.Glu197Lys missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245461 c.2229C>T synonymous_variant 0.98
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.27
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246563 p.Leu17Trp missense_variant 0.17
embB 4246567 c.54_55insT frameshift_variant 0.31
embB 4248324 p.Ala604Gly missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0