TB-Profiler result

Run: SRR19303788
Summary

Run ID: SRR19303788

Sample name:

Date: 2024-10-04T19:36:10.576704

Number of reads: 1197183

Percentage reads mapped: 40.89

Median coverage: 35.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) RD219 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
rpoC 764428 c.1059G>T synonymous_variant 0.15 rifampicin
rpoC 764461 p.Glu364Asp missense_variant 0.16 rifampicin
rpoC 764479 c.1110G>A synonymous_variant 0.15 rifampicin
rpoC 764485 c.1116G>C synonymous_variant 0.16 rifampicin
rpoC 764498 p.Ser377Ala missense_variant 0.27 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.32 rifampicin
rpoC 764537 p.Pro390Val missense_variant 0.37 rifampicin
rpoC 764540 p.Val391Ile missense_variant 0.36 rifampicin
rpoC 764548 c.1179G>C synonymous_variant 0.34 rifampicin
rpoC 764549 p.Pro394Ala missense_variant 0.34 rifampicin
rpoC 764552 p.Gly395Asn missense_variant 0.34 rifampicin
rpoC 764557 p.Asn396Lys missense_variant 0.34 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>C synonymous_variant 0.35 rifampicin
rpoC 764576 p.Ser403Ala missense_variant 0.35 rifampicin Uncertain significance
rpoC 764581 c.1212T>C synonymous_variant 0.35 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.37 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.44 rifampicin
rpoC 764629 c.1260G>A synonymous_variant 0.42 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764644 c.1275G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764656 c.1287C>T synonymous_variant 0.23 rifampicin
rpoC 764671 c.1302G>C synonymous_variant 0.17 rifampicin
rpoC 764672 p.Gln435Glu missense_variant 0.17 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.17 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
fbiC 1303747 p.Thr273Ala missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.48 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
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