TB-Profiler result

Run: ERR4812773
Summary

Run ID: ERR4812773

Sample name:

Date: 01-04-2023 12:19:30

Number of reads: 484007

Percentage reads mapped: 98.21

Strain: lineage4.1.2.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.98
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 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326278 p.Ser399* stop_gained 1.0 ethionamide
gid 4407985 p.Gly73Ala missense_variant 1.0 streptomycin
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781751 c.192G>T synonymous_variant 0.11
fbiC 1304808 c.1878C>A synonymous_variant 0.18
fbiC 1304866 p.Gly646Trp missense_variant 0.17
embR 1416992 p.Lys119Arg missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222109 c.1056C>A synonymous_variant 0.13
Rv1979c 2222501 p.Ala222Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
Rv2752c 3064821 c.1371C>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641557 p.Ser8Cys missense_variant 0.17
rpoA 3877929 c.579C>A synonymous_variant 0.11
rpoA 3878619 c.-112A>C upstream_gene_variant 0.3
clpC1 4040330 c.375C>A synonymous_variant 0.14
panD 4044326 c.-45C>A upstream_gene_variant 0.17
embC 4241659 c.1797G>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249136 p.Val875Phe missense_variant 0.15
aftB 4267873 p.Gln322Glu missense_variant 0.85
whiB6 4338595 c.-75delG upstream_gene_variant 1.0