TB-Profiler result

Run: ERR323082
Summary

Run ID: ERR323082

Sample name:

Date: 01-04-2023 00:50:29

Number of reads: 3770176

Percentage reads mapped: 99.6

Strain: lineage4.3.4.2.1;lineage4.1.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.69
lineage4.1 Euro-American T;X;H None 0.3
lineage4.1.2 Euro-American T;H None 0.29
lineage4.3.4 Euro-American (LAM) LAM RD174 0.72
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.7
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.76
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 1673425 c.-15C>T upstream_gene_variant 0.18 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
gyrB 5611 c.372C>T synonymous_variant 0.72
gyrB 6140 p.Val301Leu missense_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.74
rpoC 765150 p.Gly594Glu missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417140 p.Ala70Ser missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673249 c.-191C>T upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747022 p.Val193Ile missense_variant 0.29
ribD 2987307 p.Ala157Pro missense_variant 0.25
thyA 3073806 c.666C>G synonymous_variant 0.26
thyA 3073868 p.Thr202Ala missense_variant 0.68
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448894 p.Tyr131Asp missense_variant 0.33
Rv3083 3449642 p.Asn380Ser missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.6
fbiA 3641164 p.Ile208Val missense_variant 0.38
alr 3840719 c.702A>G synonymous_variant 0.7
clpC1 4038287 c.2418C>T synonymous_variant 0.62
clpC1 4038857 c.1848C>A synonymous_variant 0.28
embC 4242425 p.Arg855Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.23
aftB 4268861 c.-25T>C upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.77