TB-Profiler result

Run: ERR13432057
Summary

Run ID: ERR13432057

Sample name:

Date: 2025-02-11T18:55:23.782732

Number of reads: 4015168

Percentage reads mapped: 99.62

Median coverage: 114.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance Mutation from literature
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 Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761606 c.1800C>G synonymous_variant 0.11 rifampicin
rpoB 761636 c.1830G>T synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.11 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.14 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764830 c.1461C>G synonymous_variant 0.14 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766804 c.3435A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766843 c.3474T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.14 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.13 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.14 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.12 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781892 c.333A>G synonymous_variant 0.11 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.11 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.11 streptomycin
rplC 800612 c.-197A>G upstream_gene_variant 0.13 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.13 linezolid
rplC 800648 c.-161A>C upstream_gene_variant 0.13 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.12 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833874 c.333T>C synonymous_variant 0.17 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.22 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.2 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834836 p.Met432Thr missense_variant 1.0 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
folC 2746340 p.Ala420Val missense_variant 1.0 para-aminosalicylic_acid
Rv2752c 3065039 c.1071_1152delGATCGGCGCCAGAGTCGTCACCAACGCCCAAGCAAGGGTGCATGTTTCCGGCCACGCGTACGCCGGTGAGCTGCTGTTCCTC frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877613 p.Ile299Val missense_variant 0.12 rifampicin
rpoA 3877638 c.870T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3877656 c.852T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.14 rifampicin
rpoA 3877677 p.Ala277Ser missense_variant 0.12 rifampicin
rpoA 3877680 c.828G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoA 3877686 c.822A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877743 c.765T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038695 c.2010C>G synonymous_variant 0.11 pyrazinamide
clpC1 4038701 c.2004G>C synonymous_variant 0.11 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.11 pyrazinamide
clpC1 4038707 c.1998C>G synonymous_variant 0.11 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.11 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.12 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R