TB-Profiler result

Run: ERR9027230
Summary

Run ID: ERR9027230

Sample name:

Date: 02-04-2023 09:19:11

Number of reads: 1121232

Percentage reads mapped: 97.35

Strain: lineage4.3.3;lineage4.1.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.47
lineage4.1.2 Euro-American T;H None 0.49
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.48
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.55
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 0.5 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.22 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.47 isoniazid, ethionamide
tlyA 1918160 p.Leu74Pro missense_variant 0.39 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.6 pyrazinamide, pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.43 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 8040 p.Gly247Ser missense_variant 0.71
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.28
mshA 575423 p.Arg26Cys missense_variant 0.59
mshA 575679 p.Asn111Ser missense_variant 0.3
rpoB 760115 c.309C>T synonymous_variant 0.42
rpoC 764931 p.Ala521Asp missense_variant 0.38
rpoC 764995 c.1626C>G synonymous_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 0.68
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.47
fbiC 1304962 p.Trp678Gly missense_variant 0.36
Rv1258c 1406099 c.1242C>A synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.62
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289878 c.-637C>A upstream_gene_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 0.61
kasA 2518919 p.Gly269Ser missense_variant 0.43
eis 2715340 c.-8C>T upstream_gene_variant 0.48
folC 2746340 p.Ala420Val missense_variant 0.36
pepQ 2859876 c.543C>T synonymous_variant 0.11
ribD 2986827 c.-12G>A upstream_gene_variant 0.55
thyA 3073868 p.Thr202Ala missense_variant 0.49
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449002 p.Gln167* stop_gained 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642265 p.Gly244Glu missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 0.42
clpC1 4038968 c.1737G>A synonymous_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.44
embA 4245546 p.Phe772Val missense_variant 0.15
embB 4245653 c.-861C>T upstream_gene_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.12
whiB6 4338594 c.-73T>G upstream_gene_variant 0.49
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407790 p.Ala138Val missense_variant 0.55
gid 4408156 p.Leu16Arg missense_variant 0.61