TB-Profiler result

Run: ERR3283048
Summary

Run ID: ERR3283048

Sample name:

Date: 2024-10-04T05:14:56.987891

Number of reads: 132708

Percentage reads mapped: 4.08

Median coverage: 3.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.98
lineage4.9 Euro-American (H37Rv-like) None 0.98
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embB p.Leu359Ile Uncertain significance Mutation from literature
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
embB 4247588 p.Leu359Ile missense_variant 0.7 ethambutol 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
mshA 575713 c.366G>A synonymous_variant 0.92 isoniazid
ethionamide
mshA 575719 c.372C>T synonymous_variant 0.92 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
mshA 575734 c.387T>G synonymous_variant 0.9 isoniazid
ethionamide
mshA 575746 c.399C>G synonymous_variant 1.0 isoniazid
ethionamide
mshA 575752 c.405G>A synonymous_variant 0.91 isoniazid Not assoc w R - Interim
ethionamide
mshA 575771 p.Val142Ser missense_variant 1.0 isoniazid
ethionamide
mshA 575779 c.432A>G synonymous_variant 1.0 isoniazid
ethionamide
rpoB 761063 c.1257C>G synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 1.0 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 1.0 rifampicin
rpoB 762062 c.2256T>C synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 762218 c.2412T>G synonymous_variant 0.9 rifampicin
rpoC 764893 c.1524T>C synonymous_variant 0.9 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 1.0 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpsL 781715 c.156T>C synonymous_variant 0.85 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.83 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.82 streptomycin
rpsL 781751 c.192G>C synonymous_variant 0.69 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.85 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.69 streptomycin
rpsL 781793 c.234G>C synonymous_variant 0.67 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.92 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.92 streptomycin
fbiC 1303995 c.1065C>T synonymous_variant 0.69 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304001 c.1071C>G synonymous_variant 0.69 pretomanid
delamanid
clofazimine
fbiC 1304008 c.1078T>C synonymous_variant 0.79 pretomanid
delamanid
clofazimine
fbiC 1304034 c.1104A>G synonymous_variant 0.67 pretomanid
delamanid
clofazimine
fbiC 1304040 c.1110C>G synonymous_variant 0.73 pretomanid
delamanid
clofazimine
fbiC 1304046 c.1116C>G synonymous_variant 0.64 pretomanid
delamanid
clofazimine
fbiC 1304049 c.1119T>G synonymous_variant 0.7 pretomanid
delamanid
clofazimine
sigE 1364763 c.351T>C synonymous_variant 1.0 pyrazinamide
sigE 1364767 c.355A>C synonymous_variant 1.0 pyrazinamide
sigE 1364784 c.372C>G synonymous_variant 0.9 pyrazinamide
sigE 1364802 c.390C>A synonymous_variant 0.92 pyrazinamide
sigE 1364811 c.399A>G synonymous_variant 0.91 pyrazinamide
sigE 1364820 c.408A>G synonymous_variant 0.9 pyrazinamide
sigE 1364835 c.423C>G synonymous_variant 0.8 pyrazinamide
sigE 1364839 c.427T>C synonymous_variant 0.9 pyrazinamide
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.61 capreomycin Not assoc w R
linezolid Uncertain significance
ndh 2102683 c.360T>C synonymous_variant 1.0 isoniazid
delamanid
ethionamide
kasA 2518567 c.453G>C synonymous_variant 1.0 isoniazid
kasA 2518570 c.456G>C synonymous_variant 0.8 isoniazid
kasA 2518574 p.Ile154Val missense_variant 1.0 isoniazid
kasA 2518609 p.Met165Ile missense_variant 0.85 isoniazid
kasA 2518621 c.507G>A synonymous_variant 0.67 isoniazid
kasA 2518642 c.528A>G synonymous_variant 0.9 isoniazid
thyX 3067355 c.591A>C synonymous_variant 0.9 para-aminosalicylic_acid
lpqB 3625291 c.-381A>G upstream_gene_variant 0.8 rifampicin
bedaquiline
lpqB 3625345 c.-435T>C upstream_gene_variant 0.7 rifampicin
bedaquiline
mtrB 3625592 p.Ser341Asn missense_variant 0.9 rifampicin
bedaquiline
lpqB 3625594 c.-684T>C upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625602 c.-692T>C upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625606 c.-696C>T upstream_gene_variant 0.7 rifampicin
bedaquiline
lpqB 3625612 c.-702G>C upstream_gene_variant 0.8 rifampicin
bedaquiline
mtrB 3625616 p.Arg333Ala missense_variant 1.0 rifampicin
bedaquiline
lpqB 3625624 c.-714C>G upstream_gene_variant 0.8 rifampicin
bedaquiline
lpqB 3625627 c.-717C>T upstream_gene_variant 0.7 rifampicin
bedaquiline
lpqB 3625648 c.-738T>C upstream_gene_variant 0.9 rifampicin
bedaquiline
lpqB 3625663 c.-753G>C upstream_gene_variant 1.0 rifampicin
bedaquiline
rpoA 3877686 c.822A>G synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoA 3878976 c.-469A>G upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3878989 c.-482G>C upstream_gene_variant 0.67 rifampicin
rpoA 3878998 c.-491C>G upstream_gene_variant 0.92 rifampicin Uncertain significance
rpoA 3879013 c.-506A>G upstream_gene_variant 0.92 rifampicin
rpoA 3879016 c.-509A>G upstream_gene_variant 0.92 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.82 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.8 rifampicin
embB 4247500 c.987C>G synonymous_variant 0.9 ethambutol
embB 4247512 c.999T>C synonymous_variant 1.0 ethambutol
embB 4247536 c.1023C>G synonymous_variant 0.7 ethambutol
embB 4247554 c.1041T>C synonymous_variant 1.0 ethambutol
embB 4247567 c.1054C>T synonymous_variant 0.9 ethambutol
embB 4247587 c.1074G>A synonymous_variant 0.7 ethambutol
embB 4247603 c.1090C>T synonymous_variant 0.7 ethambutol
embB 4248095 c.1582_1584delCTCinsTTG synonymous_variant 0.7 ethambutol
embB 4248118 c.1605T>C synonymous_variant 0.82 ethambutol
embB 4248127 c.1614G>C synonymous_variant 0.7 ethambutol