TB-Profiler result

Run: ERR2041687
Summary

Run ID: ERR2041687

Sample name:

Date: 18-08-2022 09:22:55

Number of reads: 657686

Percentage reads mapped: 97.88

Strain: lineage4.2.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.97
lineage4.2.2.1 Euro-American LAM7-TUR None 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_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
gyrB 6026 p.His263Asn missense_variant 0.12
gyrB 6070 c.831C>T synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9525 p.Val742Leu missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoC 765421 c.2052C>A synonymous_variant 0.12
rpoC 766135 c.2766G>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305058 p.Tyr710Asn missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473859 n.202T>C non_coding_transcript_exon_variant 0.18
rrl 1475241 n.1584C>G non_coding_transcript_exon_variant 1.0
fabG1 1673221 c.-219C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
fabG1 1674133 p.Ile232Val missense_variant 0.17
rpsA 1833427 c.-115G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155465 p.Leu216Pro missense_variant 0.13
pncA 2289483 c.-243delA upstream_gene_variant 0.12
kasA 2518907 c.793T>C synonymous_variant 0.15
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087284 c.465C>G synonymous_variant 0.12
embC 4240801 c.939C>T synonymous_variant 0.18
embC 4240803 p.Tyr314Phe missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244958 p.Ala576Thr missense_variant 1.0