TB-Profiler result

Run: ERR017777
Summary

Run ID: ERR017777

Sample name:

Date: 31-03-2023 07:55:47

Number of reads: 188992

Percentage reads mapped: 87.9

Strain: lineage4.9

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 0.97
lineage4.9 Euro-American (H37Rv-like) T1 None 0.83
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
gyrA 7582 p.Asp94Gly missense_variant 0.4 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.67 rifampicin
rpoC 765609 p.Asp747Ala missense_variant 0.4 rifampicin
pncA 2288836 p.Asp136Tyr missense_variant 0.67 pyrazinamide
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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.67
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 1.0
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.6
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.5
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.6
rrl 1476194 n.2537A>T non_coding_transcript_exon_variant 0.67
rpsA 1834177 c.636A>C synonymous_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.5
gid 4407588 c.615A>G synonymous_variant 1.0