TB-Profiler result

Run: ERR4812126
Summary

Run ID: ERR4812126

Sample name:

Date: 01-04-2023 11:52:41

Number of reads: 667279

Percentage reads mapped: 99.47

Strain:

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
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.31
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 1673423 c.-17G>T upstream_gene_variant 0.54 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 0.35
mshA 575679 p.Asn111Ser missense_variant 0.38
mshA 576108 p.Ala254Gly missense_variant 0.43
mshA 576111 p.Ala255Gly missense_variant 0.33
rpoB 760115 c.309C>T synonymous_variant 0.25
rpoB 761889 p.Val695Leu missense_variant 0.59
rpoC 765150 p.Gly594Glu missense_variant 0.37
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102404 c.639G>A synonymous_variant 0.12
ndh 2102456 p.Thr196Lys missense_variant 0.15
ndh 2102521 c.522C>A synonymous_variant 0.15
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.48
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.39
Rv2752c 3065517 c.675C>T synonymous_variant 0.59
ald 3086788 c.-32T>C upstream_gene_variant 0.35
Rv3083 3448439 c.-64delA upstream_gene_variant 0.72
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.25
fprA 3474299 p.Asp98Gly missense_variant 0.62
clpC1 4040211 p.Pro165Gln missense_variant 0.15
embC 4242803 p.Val981Leu missense_variant 0.67
embC 4242806 p.Phe982Ile missense_variant 0.67
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4248041 p.Ala510Ser missense_variant 0.12
ethA 4326996 p.Pro160Thr missense_variant 0.67
ethA 4328317 c.-844C>T upstream_gene_variant 0.39
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408365 c.-163C>T upstream_gene_variant 0.12