TB-Profiler result

Run: ERR4812878
Summary

Run ID: ERR4812878

Sample name:

Date: 01-04-2023 12:23:50

Number of reads: 5713790

Percentage reads mapped: 99.57

Strain: lineage4

Drug-resistance: MDR-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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 576222 p.Gly292Val missense_variant 0.5
mshA 576292 c.945C>T synonymous_variant 0.12
rpoB 761889 p.Val695Leu missense_variant 1.0
rpoC 764817 p.Val483Gly 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
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155751 p.Gly121Ser missense_variant 1.0
PPE35 2170317 p.Ala99Asp missense_variant 0.12
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518721 p.Glu203* stop_gained 0.14
eis 2714951 p.Arg128Trp missense_variant 0.33
folC 2747783 c.-185G>A upstream_gene_variant 0.13
pepQ 2859990 c.429G>A synonymous_variant 0.22
pepQ 2860044 c.375C>A synonymous_variant 0.17
pepQ 2860079 p.Leu114Met missense_variant 0.17
pepQ 2860095 c.324C>T synonymous_variant 0.17
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
thyX 3067564 c.382C>T synonymous_variant 0.14
Rv3083 3448439 c.-64delA upstream_gene_variant 1.0
fprA 3474299 p.Asp98Gly missense_variant 1.0
Rv3236c 3612132 p.Ala329Ser missense_variant 0.15
rpoA 3878595 c.-88C>T upstream_gene_variant 0.39
clpC1 4038167 c.2538C>T synonymous_variant 0.18
embC 4240525 c.663C>A synonymous_variant 0.5
embC 4241159 p.Ala433Thr missense_variant 0.22
embC 4242320 p.Pro820Ser missense_variant 0.17
embA 4242343 c.-890G>T upstream_gene_variant 0.25
embC 4242363 p.Gly834Val missense_variant 0.4
embA 4243681 p.Ala150Asp missense_variant 0.11
embB 4246918 c.405G>T synonymous_variant 0.19
embB 4246999 c.486C>T synonymous_variant 0.12
embB 4247738 p.Ala409Thr missense_variant 0.13
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0