TB-Profiler result

Run: SRR18593215
Summary

Run ID: SRR18593215

Sample name:

Date: 03-04-2023 19:56:32

Number of reads: 4559494

Percentage reads mapped: 97.58

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 0.96
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
gyrB 6738 p.Thr500Asn missense_variant 0.73 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7566 p.Asp89Asn missense_variant 0.89 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 0.88 rifampicin
rpoB 761155 p.Ser450Trp missense_variant 0.12 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.13 streptomycin
tlyA 1918064 c.126_127dupGG frameshift_variant 0.14 capreomycin
katG 2155169 p.Ser315Arg missense_variant 0.83 isoniazid
embB 4247574 p.Asp354Ala missense_variant 0.11 ethambutol
embB 4248002 p.Gln497Lys missense_variant 0.78 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.86 ethambutol
ethA 4326675 c.788_798delTGTTCCTGAGC frameshift_variant 0.85 ethionamide
ethA 4326721 c.752dupG frameshift_variant 0.15 ethionamide, 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
gyrB 6091 c.852G>A synonymous_variant 0.96
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 761231 c.1425C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.98
fabG1 1673162 c.-278T>C upstream_gene_variant 0.99
inhA 1674283 p.Val28Leu missense_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2155627 p.Ala162Glu missense_variant 0.11
katG 2156419 c.-308C>A upstream_gene_variant 0.84
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288832 p.His137Leu missense_variant 0.12
pncA 2289040 c.187_201dupGACTATTCCTCGTCG conservative_inframe_insertion 0.76
ahpC 2726142 c.-51G>A upstream_gene_variant 0.17
Rv2752c 3065938 p.Asp85Gly missense_variant 0.15
ald 3086966 p.Asp49Glu missense_variant 0.98
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3236c 3612047 p.Ala357Val missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326505 c.969C>G synonymous_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408139 p.Tyr22Asn missense_variant 0.89
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0