TB-Profiler result

Run: ERR1035318
Summary

Run ID: ERR1035318

Sample name:

Date: 31-03-2023 10:11:04

Number of reads: 7286199

Percentage reads mapped: 98.72

Strain: lineage4.3.4.1

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 0.97 isoniazid, ethionamide
pncA 2289055 p.Asp63His missense_variant 1.0 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
ald 3087810 c.992dupC frameshift_variant 0.86 cycloserine
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.98 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 6028 c.789C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8639 c.1338G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759608 c.-199C>T upstream_gene_variant 1.0
rpoB 761998 p.Leu731Pro missense_variant 0.99
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801066 c.258G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.15
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.16
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.25
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.28
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.17
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.17
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.18
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.14
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.12
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.23
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.21
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.3
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.21
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.14
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.13
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.11
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.18
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.23
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.17
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155721 p.Pro131Ser missense_variant 0.99
PPE35 2169320 p.Leu431Phe missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726323 p.Pro44Arg missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.99
thyA 3074492 c.-21T>C upstream_gene_variant 1.0
thyA 3074499 c.-29_-28insC upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448598 p.Ile32Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3878270 p.Leu80Val missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268982 c.-146G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0