TB-Profiler result

Run: ERR4813085
Summary

Run ID: ERR4813085

Sample name:

Date: 01-04-2023 12:31:48

Number of reads: 2816108

Percentage reads mapped: 99.54

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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
gyrA 9467 c.2166T>C synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472308 n.463T>C non_coding_transcript_exon_variant 0.12
rrs 1472483 n.638C>A non_coding_transcript_exon_variant 0.18
rrs 1472717 n.872C>A non_coding_transcript_exon_variant 0.12
rrs 1472733 n.888G>T non_coding_transcript_exon_variant 0.14
rrs 1472783 n.938G>T non_coding_transcript_exon_variant 0.14
rrl 1473979 n.322G>T non_coding_transcript_exon_variant 0.25
rrl 1474810 n.1153G>T non_coding_transcript_exon_variant 0.13
rrl 1475193 n.1536C>A non_coding_transcript_exon_variant 0.15
rrl 1476122 n.2465A>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918400 p.Asp154Ala missense_variant 1.0
katG 2154849 c.1263T>C synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714796 c.537C>T synonymous_variant 1.0
folC 2747022 p.Val193Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448702 p.Arg67Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474234 c.228C>T synonymous_variant 1.0
fbiA 3641164 p.Ile208Val missense_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408085 p.Glu40Gln missense_variant 1.0