TB-Profiler result

Run: ERR4831465
Summary

Run ID: ERR4831465

Sample name:

Date: 01-04-2023 20:57:12

Number of reads: 1776051

Percentage reads mapped: 99.82

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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Arg missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576442 p.Cys365Trp missense_variant 0.19
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 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.19
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.33
fbiA 3640375 c.-168C>A upstream_gene_variant 0.26
fbiA 3640407 c.-136G>A upstream_gene_variant 0.77
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4240420 c.558T>G synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338587 c.-81_-67delACTAGAGCTCGGAGC upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0