TB-Profiler result

Run: ERR4821851
Summary

Run ID: ERR4821851

Sample name:

Date: 01-04-2023 17:29:12

Number of reads: 1306433

Percentage reads mapped: 99.62

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 1.0
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
katG 2155355 c.756delT frameshift_variant 0.11 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
gyrA 9716 c.2415T>C synonymous_variant 0.1
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576085 c.738G>A synonymous_variant 1.0
rpoB 759861 p.Gln19Glu missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762263 c.2457C>T synonymous_variant 0.13
rpoB 763077 p.Val1091Ile missense_variant 0.11
rpoC 763553 p.Cys62Arg missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766155 p.Ala929Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775928 p.Asn851Lys missense_variant 0.1
mmpL5 777274 p.Val403Phe missense_variant 0.12
mmpS5 778821 p.Arg29Cys missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673719 p.Asp94Asn missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102688 p.Ala119Thr missense_variant 0.11
katG 2154446 p.Ala556Thr missense_variant 0.11
PPE35 2167916 c.2696delT frameshift_variant 0.12
PPE35 2168463 p.Pro717His missense_variant 0.11
Rv1979c 2223289 c.-125G>A upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289869 c.-628G>T upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ribD 2987450 p.Glu204Asp missense_variant 1.0
Rv2752c 3067100 c.-909G>C upstream_gene_variant 0.12
thyX 3067928 c.18G>T synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038170 c.2535G>T synonymous_variant 1.0
clpC1 4039104 p.Arg534His missense_variant 0.11
embC 4241653 c.1791C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0