TB-Profiler result

Run: ERR2652998

Summary

Run ID: ERR2652998

Sample name:

Date: 31-03-2023 22:26:13

Number of reads: 926833

Percentage reads mapped: 99.68

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.97 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 6227 p.Lys330* stop_gained 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>A synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168483 c.2130C>T synonymous_variant 0.11
PPE35 2169091 p.Val508Leu missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289070 p.Phe58Val missense_variant 1.0
Rv3083 3449900 p.Tyr466Cys missense_variant 0.11
fbiB 3641831 c.297C>T synonymous_variant 0.11
fbiB 3641867 c.333C>T synonymous_variant 0.11
alr 3841071 p.Gly117Asp missense_variant 1.0
clpC1 4040525 c.180C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243977 p.Ala249Thr missense_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407590 p.Ala205Thr missense_variant 1.0
gid 4407949 p.Asp85Ala missense_variant 1.0