TB-Profiler result

Run: ERR2516136
Summary

Run ID: ERR2516136

Sample name:

Date: 31-03-2023 21:18:54

Number of reads: 968521

Percentage reads mapped: 99.2

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Val missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326082 c.1391dupA frameshift_variant 1.0 ethionamide, ethionamide
gid 4407830 p.Gln125* stop_gained 0.98 streptomycin
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 6428 p.Glu397* stop_gained 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 759657 c.-150G>T upstream_gene_variant 0.1
rpoC 764819 p.Trp484Gly missense_variant 1.0
rpoC 765008 p.Leu547Val missense_variant 1.0
rpoC 766085 p.Pro906Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776666 p.Asp605Glu missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.17
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.13
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.12
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.13
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.14
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.14
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.14
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.15
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474448 n.791T>C non_coding_transcript_exon_variant 0.17
rrl 1474451 n.794T>C non_coding_transcript_exon_variant 0.18
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.17
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.15
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.15
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.14
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.12
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.14
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.15
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.15
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.15
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168416 p.Gly733Trp missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087658 c.840dupG frameshift_variant 1.0
whiB7 3568730 c.-52_-51insC upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
embC 4241726 p.Phe622Leu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245841 p.Val870Glu missense_variant 0.11
embB 4246532 p.Arg7Gly missense_variant 0.1
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0