TB-Profiler result

Run: ERR8774265
Summary

Run ID: ERR8774265

Sample name:

Date: 02-04-2023 08:25:55

Number of reads: 5769179

Percentage reads mapped: 98.67

Strain: lineage4.6.2.2

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761127 p.Ser441Gln missense_variant 0.98 rifampicin
katG 2155411 p.Gly234Glu missense_variant 0.99 isoniazid
ahpC 2726119 c.-74G>A upstream_gene_variant 0.99 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
pncA 2288479 c.158_*201del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472028 n.183A>G non_coding_transcript_exon_variant 0.12
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.17
rrl 1473810 n.153C>A non_coding_transcript_exon_variant 0.25
rrl 1474108 n.451C>T non_coding_transcript_exon_variant 0.15
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.17
rrl 1474762 n.1105G>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 0.99
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289083 c.159C>T synonymous_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 0.99
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 0.99
embA 4242550 c.-683C>G upstream_gene_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.98
aftB 4267272 p.Lys522Arg missense_variant 0.99
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0