TB-Profiler result

Run: ERR4830778
Summary

Run ID: ERR4830778

Sample name:

Date: 01-04-2023 20:26:42

Number of reads: 3630435

Percentage reads mapped: 99.09

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 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 7563 p.Gly88Cys 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 0.72 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674481 p.Ser94Ala missense_variant 0.22 isoniazid, ethionamide
ald 3087252 c.436_437dupGC frameshift_variant 0.13 cycloserine
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327126 p.Trp116* stop_gained 0.6 ethionamide
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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.17
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 767123 p.Val1252Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777792 p.Ala230Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.14
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.12
rrs 1472771 n.926G>A non_coding_transcript_exon_variant 0.13
rrl 1473771 n.114T>A non_coding_transcript_exon_variant 0.17
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.2
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.22
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.29
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.29
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.29
rrl 1474376 n.719T>A non_coding_transcript_exon_variant 0.4
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.5
rrl 1475610 n.1953G>A non_coding_transcript_exon_variant 0.33
rrl 1476641 n.2984T>C non_coding_transcript_exon_variant 0.12
rrl 1476716 n.3059A>G non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155667 p.Trp149Arg missense_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288973 p.Ile90Asn missense_variant 1.0
ahpC 2726142 c.-51G>A upstream_gene_variant 1.0
Rv2752c 3064688 c.1503dupC frameshift_variant 0.99
ald 3087827 c.1010delC frameshift_variant 0.19
fbiD 3339734 p.Ala206Gly missense_variant 0.23
fbiD 3339740 p.Ala208Val missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0