TB-Profiler result

Run: SRR18572454
Summary

Run ID: SRR18572454

Sample name:

Date: 2024-10-04T19:35:46.667252

Number of reads: 4730903

Percentage reads mapped: 89.63

Median coverage: 117.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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 rpoB p.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
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
rpoB 761127 p.Ser441Ala missense_variant 0.11 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin 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
rpoB 761051 c.1245G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761084 c.1278C>G synonymous_variant 0.12 rifampicin
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.12 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.12 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.13 rifampicin
rpoB 761132 c.1326G>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.11 rifampicin Uncertain significance
rpoB 762122 p.Asp772Glu missense_variant 0.1 rifampicin
rpoB 762125 p.Glu773Asp missense_variant 0.11 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 0.1 rifampicin Uncertain significance
rpoB 762929 c.3123G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763621 c.252C>G synonymous_variant 0.11 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763705 c.336G>C synonymous_variant 0.11 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>G synonymous_variant 0.1 rifampicin
rpoC 764536 c.1167G>C synonymous_variant 0.11 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764560 c.1191T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764572 c.1203G>C synonymous_variant 0.11 rifampicin
rpoC 764575 c.1206T>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.1 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.11 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.15 rifampicin
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.15 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.15 rifampicin
rpoC 764650 c.1281G>C synonymous_variant 0.15 rifampicin
rpoC 764665 c.1296C>G synonymous_variant 0.15 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764681 p.Leu438Met missense_variant 0.18 rifampicin
rpoC 764706 p.Leu446Gln missense_variant 0.17 rifampicin Uncertain significance
rpoC 764713 c.1344G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764731 c.1362G>C synonymous_variant 0.11 rifampicin
fbiC 1305250 p.Arg774Gly missense_variant 0.17 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.31 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance