TB-Profiler result

Run: ERR11082097
Summary

Run ID: ERR11082097

Sample name:

Date: 10-04-2023 00:12:55

Number of reads: 1774917

Percentage reads mapped: 99.56

Strain: 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
lineage4.1 Euro-American T;X;H None 0.16
lineage4.1.2 Euro-American T;H None 0.17
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.23
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 761095 p.Leu430Pro missense_variant 0.84 rifampicin
rpoB 761141 p.His445Gln missense_variant 0.88 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.2 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.17 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289231 p.Leu4Ser missense_variant 0.16 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.88 para-aminosalicylic_acid
embB 4247431 p.Met306Ile missense_variant 0.85 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.16 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 7892 c.591G>A synonymous_variant 0.86
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620619 c.729G>A synonymous_variant 0.88
rpoB 760115 c.309C>T synonymous_variant 0.28
rpoC 765150 p.Gly594Glu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407109 p.Ala78Thr missense_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.15
eis 2715338 c.-6G>T upstream_gene_variant 0.21
ribD 2986827 c.-12G>A upstream_gene_variant 0.19
thyA 3074365 p.Tyr36Ser missense_variant 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475125 c.1119G>A synonymous_variant 0.84
alr 3841362 p.Thr20Met missense_variant 0.77
rpoA 3878575 c.-68C>T upstream_gene_variant 0.69
clpC1 4038318 p.Pro796Leu missense_variant 0.89
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.21
embB 4247028 p.Leu172Pro missense_variant 0.11
ethA 4327310 p.Ser55Cys missense_variant 0.89
ethA 4327378 p.Tyr32* stop_gained 0.84
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407980 p.Pro75Ser missense_variant 0.62