TB-Profiler result

Run: SRR26159063
Summary

Run ID: SRR26159063

Sample name:

Date: 2024-04-16T01:47:44.490928

Number of reads: 429093

Percentage reads mapped: 99.4

Median coverage: 0.0

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 c.1327_1329delTTGinsCC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761133 c.1327_1329delTTGinsCC frameshift_variant&missense_variant 0.93 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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 6565 c.-737G>C upstream_gene_variant 0.91 levofloxacin
moxifloxacin
gyrA 6571 c.-731T>C upstream_gene_variant 0.97 levofloxacin
moxifloxacin
rpoB 760961 c.1155C>T synonymous_variant 0.93 rifampicin
rpoB 760991 c.1185G>C synonymous_variant 0.93 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 761027 c.1221A>G synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>T synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 761063 c.1257C>G synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 761094 c.1288C>T synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.9 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.92 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoB 761171 c.1365C>T synonymous_variant 0.91 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>G synonymous_variant 0.96 rifampicin
rpoB 761192 c.1386C>G synonymous_variant 0.95 rifampicin
rpoB 761195 c.1389G>C synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoB 761234 c.1428G>C synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 761286 c.1480C>T synonymous_variant 1.0 rifampicin
rpoB 761300 c.1494G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 761345 c.1539G>C synonymous_variant 0.99 rifampicin
rpoB 761346 p.Val514Ile missense_variant 0.99 rifampicin
rpoB 761354 c.1548C>T synonymous_variant 0.99 rifampicin
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472313 n.468delGinsCA non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.99 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.96 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.98 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473417 n.-241C>T upstream_gene_variant 0.99 capreomycin
linezolid
rrl 1473421 n.-237G>A upstream_gene_variant 0.99 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476035 n.2378G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476118 n.2461G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid