TB-Profiler result

Run: ERR11465351
Summary

Run ID: ERR11465351

Sample name:

Date: 2024-10-05T01:17:39.153642

Number of reads: 3316052

Percentage reads mapped: 99.18

Median coverage: 70.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 0.95
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 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
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
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 8813 p.Asp504Glu missense_variant 0.11 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.97 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.98 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575893 c.546C>G synonymous_variant 0.17 isoniazid
ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
mmaA3 737358 c.792A>C synonymous_variant 0.16 isoniazid
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 760406 c.600G>C synonymous_variant 0.12 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760611 c.805_807delTTGinsCTC synonymous_variant 0.17 rifampicin
rpoB 761892 p.Ile696Val missense_variant 0.11 rifampicin
rpoB 761930 c.2124G>C synonymous_variant 0.14 rifampicin
rpoB 762083 c.2277T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762131 c.2325C>G synonymous_variant 0.12 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.13 rifampicin Not assoc w R
rpoB 763040 c.3234C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763103 c.-267G>C upstream_gene_variant 0.13 rifampicin
rpoB 763115 c.3309T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765499 c.2130C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766345 c.2976T>C synonymous_variant 0.12 rifampicin
rpoC 766348 c.2979A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 766369 c.3000C>G synonymous_variant 0.15 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.18 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.18 rifampicin
rpoC 766393 c.3024C>G synonymous_variant 0.15 rifampicin
rpoC 766426 c.3057C>T synonymous_variant 0.18 rifampicin
rpoC 766429 c.3060C>G synonymous_variant 0.19 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.17 rifampicin
rpoC 766459 c.3090G>C synonymous_variant 0.13 rifampicin
rpoC 766516 c.3147C>G synonymous_variant 0.13 rifampicin
rpoC 766517 p.Thr1050Ser missense_variant 0.13 rifampicin
rpoC 766528 c.3159T>G synonymous_variant 0.12 rifampicin
rpoC 766540 p.Asp1057Glu missense_variant 0.11 rifampicin
rpoC 766543 c.3174C>T synonymous_variant 0.13 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.12 rifampicin
rpoC 766774 c.3405T>C synonymous_variant 0.17 rifampicin
rpoC 766837 c.3468G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766843 c.3474T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
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 781733 c.174G>C synonymous_variant 0.12 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.15 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674486 c.285T>C synonymous_variant 0.14 isoniazid
ethionamide
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
PPE35 2169902 p.Leu237Phe missense_variant 0.13 pyrazinamide
PPE35 2169910 p.Asn235Tyr missense_variant 0.16 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
kasA 2518783 c.669T>C synonymous_variant 0.15 isoniazid
kasA 2518795 c.681C>G synonymous_variant 0.14 isoniazid
kasA 2518811 p.Asp233Asn missense_variant 0.13 isoniazid
kasA 2518816 c.702C>T synonymous_variant 0.13 isoniazid
kasA 2518825 c.711T>C synonymous_variant 0.13 isoniazid
kasA 2518843 c.729T>C synonymous_variant 0.14 isoniazid
kasA 2518847 p.Leu245Met missense_variant 0.14 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin
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
clpC1 4038596 c.2109A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.14 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4241104 c.1242G>A synonymous_variant 0.12 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.57 ethambutol Uncertain significance
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