TB-Profiler result

Run: ERR2653143
Summary

Run ID: ERR2653143

Sample name:

Date: 31-03-2023 22:35:23

Number of reads: 7269391

Percentage reads mapped: 97.79

Strain: lineage4.3.2

Drug-resistance: Pre-XDR-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 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
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
gyrB 6620 p.Asp461Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
pncA 2288941 c.300delC frameshift_variant 0.34 pyrazinamide
embB 4247574 p.Asp354Ala 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575471 p.Asp42Tyr missense_variant 1.0
rpoB 759939 p.Pro45Ala missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407044 p.Asp99Glu missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153977 p.Gly712Ala missense_variant 0.33
katG 2154850 p.Gly421Ala missense_variant 0.99
katG 2156489 c.-378C>A upstream_gene_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087292 c.474_475dupGC frameshift_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612361 c.756C>T synonymous_variant 0.99
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269306 p.Phe176Leu missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
whiB6 4337650 c.-186_*520del transcript_ablation 1.0