TB-Profiler result

Run: ERR11050207
Summary

Run ID: ERR11050207

Sample name:

Date: 02-04-2023 16:02:32

Number of reads: 3554526

Percentage reads mapped: 99.81

Strain: lineage4.3.4.2

Drug-resistance: MDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 761109 p.Asp435Tyr missense_variant 0.98 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243222 c.-11C>A upstream_gene_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
fgd1 491683 p.Val301Leu missense_variant 1.0
mshA 576106 c.759C>G synonymous_variant 0.33
mshA 576113 p.Arg256Gly missense_variant 0.3
mshA 576442 p.Cys365Trp missense_variant 0.36
mshA 576453 p.Val369Gly missense_variant 0.27
mshA 576456 p.Val370Gly missense_variant 0.36
mshA 576468 p.Val374Gly missense_variant 0.27
mshA 576489 p.Val381Gly missense_variant 0.33
mshA 576606 p.Ala420Gly missense_variant 0.36
mshA 576613 c.1266A>C synonymous_variant 0.5
mshA 576616 c.1269G>C synonymous_variant 0.4
mshA 576618 p.His424Pro missense_variant 0.33
rpoC 764367 p.Gly333Ala missense_variant 0.23
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.34
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303157 p.His76Pro missense_variant 0.24
embR 1416430 c.918G>C synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475795 n.2138A>C non_coding_transcript_exon_variant 0.18
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.21
fabG1 1673553 p.Asp38Glu missense_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170386 p.Leu76Arg missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.53
Rv2752c 3064823 p.Val457Leu missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 1.0
fbiD 3339751 p.Ala212Pro missense_variant 0.44
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474213 p.Lys69Asn missense_variant 0.19
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612268 c.849C>T synonymous_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.85
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.32
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243682 c.450T>G synonymous_variant 0.2
embB 4246527 p.Ala5Gly missense_variant 0.52
embB 4247016 p.Ser168Trp missense_variant 0.27
embB 4247020 c.507C>G synonymous_variant 0.38
embB 4248328 c.1815G>C synonymous_variant 0.19
aftB 4267981 p.Arg286Gly missense_variant 0.33
whiB6 4338200 p.Asp108His missense_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0