TB-Profiler result

Run: SRR998817

Summary

Run ID: SRR998817

Sample name:

Date: 04-04-2023 23:37:20

Number of reads: 607564

Percentage reads mapped: 99.36

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 1.0
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
fabG1 1673425 c.-15C>T 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 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761913 p.Asp703Tyr missense_variant 0.12
rpoC 764219 p.Gly284Ser missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776450 c.2031C>T synonymous_variant 0.11
mmpL5 778678 c.-198C>A upstream_gene_variant 0.12
mmpL5 778891 c.-411C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801142 p.Val112Phe missense_variant 0.12
fbiC 1303266 c.336C>T synonymous_variant 0.18
fbiC 1305117 c.2187T>C synonymous_variant 0.14
Rv1258c 1406597 c.744G>T synonymous_variant 0.11
embR 1416432 p.Ala306Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102640 p.Ala135Thr missense_variant 0.12
katG 2154300 p.Leu604Phe missense_variant 0.17
katG 2154747 c.1365T>C synonymous_variant 0.12
katG 2155324 p.Ala263Glu missense_variant 0.13
PPE35 2169783 p.Thr277Lys missense_variant 1.0
Rv1979c 2221926 c.1239C>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519243 p.Asp377Tyr missense_variant 0.13
ahpC 2726006 c.-187C>A upstream_gene_variant 0.12
folC 2746465 c.1134G>T synonymous_variant 0.13
folC 2747100 p.Pro167Thr missense_variant 0.14
pepQ 2859786 c.633G>T synonymous_variant 0.2
pepQ 2859849 p.Phe190Leu missense_variant 0.22
thyX 3067425 p.Val174Ala missense_variant 0.12
thyX 3067954 c.-9G>C upstream_gene_variant 0.22
thyA 3073916 p.His186Tyr missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448844 p.Cys114Phe missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475032 c.1026C>T synonymous_variant 0.11
whiB7 3568494 c.186C>A synonymous_variant 0.14
whiB7 3568618 p.His21Arg missense_variant 0.14
alr 3840786 p.Ala212Val missense_variant 0.12
panD 4044007 p.Thr92Arg missense_variant 0.12
embC 4241847 p.Thr662Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4248451 p.Trp646Cys missense_variant 0.12
ethR 4327279 c.-270T>C upstream_gene_variant 0.12
whiB6 4338448 p.Ala25Val missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0