TB-Profiler result

Run: ERR4813328
Summary

Run ID: ERR4813328

Sample name:

Date: 01-04-2023 12:40:37

Number of reads: 2256903

Percentage reads mapped: 91.69

Strain: lineage4

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
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 0.99 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
mshA 575188 c.-160G>T upstream_gene_variant 0.12
mshA 575198 c.-150C>A upstream_gene_variant 0.13
mshA 575567 p.Gln74* stop_gained 0.13
mshA 576746 p.Gly467Cys missense_variant 0.25
rpoB 761889 p.Val695Leu missense_variant 1.0
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 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834876 c.1335G>T synonymous_variant 0.12
tlyA 1917909 c.-31C>A upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715100 p.Pro78Gln missense_variant 0.2
folC 2747389 c.210G>T synonymous_variant 0.12
pepQ 2859777 c.642C>A synonymous_variant 0.12
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
fbiD 3339434 p.Gly106Val missense_variant 0.4
Rv3083 3448439 c.-64delA upstream_gene_variant 1.0
fprA 3474299 p.Asp98Gly missense_variant 1.0
Rv3236c 3612152 p.Gly322Glu missense_variant 0.12
fbiB 3641564 c.30G>T synonymous_variant 0.12
fbiB 3641574 p.Ile14Val missense_variant 0.11
fbiB 3642723 p.Trp397Gly missense_variant 0.12
rpoA 3878595 c.-88C>T upstream_gene_variant 0.5
clpC1 4040188 p.Gln173Lys missense_variant 0.12
embC 4240539 p.Pro226His missense_variant 0.67
embC 4241134 c.1272G>T synonymous_variant 0.25
embA 4243812 p.Arg194Trp missense_variant 0.12
embA 4244724 p.Asp498Tyr missense_variant 0.15
embA 4244771 c.1539G>A synonymous_variant 0.22
embB 4245524 c.-990G>A upstream_gene_variant 0.18
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338209 p.Pro105Thr missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0