TB-Profiler result

Run: ERR4831945
Summary

Run ID: ERR4831945

Sample name:

Date: 01-04-2023 21:13:33

Number of reads: 861358

Percentage reads mapped: 99.51

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
gid 4408087 c.115delC frameshift_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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.3
ccsA 620029 c.139C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302778 c.-153G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472449 n.604C>A non_coding_transcript_exon_variant 0.13
rrl 1474661 n.1004G>T non_coding_transcript_exon_variant 0.2
rrl 1475930 n.2273G>T non_coding_transcript_exon_variant 0.22
rrl 1476352 n.2695T>C non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918059 c.120C>A synonymous_variant 0.29
katG 2155751 p.Gly121Ser missense_variant 1.0
PPE35 2169854 c.759T>G synonymous_variant 0.18
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.17
fbiD 3339324 c.207G>T synonymous_variant 0.17
fbiD 3339544 c.427C>A synonymous_variant 0.12
Rv3083 3448988 p.Arg162Gln missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878336 p.Gly58Arg missense_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embC 4242095 p.Ala745Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0