TB-Profiler result

Run: SRR22249687
Summary

Run ID: SRR22249687

Sample name:

Date: 2024-10-04T22:39:09.616938

Number of reads: 3754292

Percentage reads mapped: 98.67

Median coverage: 110.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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 0.99
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
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
gyrB 6815 p.Lys526Gln missense_variant 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761477 c.1671C>G synonymous_variant 0.13 rifampicin
rpoC 763696 c.327T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.14 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.15 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.12 rifampicin
rpoC 763835 p.Ala156Met missense_variant 0.13 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.14 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>A synonymous_variant 0.13 rifampicin
rpoC 764551 c.1182G>C synonymous_variant 0.13 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765772 c.2403C>G synonymous_variant 0.12 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.14 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.14 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.13 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.14 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.14 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.13 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 781832 c.273T>C synonymous_variant 0.12 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474960 n.1303C>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474965 n.1308G>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rpsA 1833661 c.120A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.13 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169902 c.711G>C synonymous_variant 0.12 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2783181 p.Leu288Val missense_variant 0.98 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
thyX 3067697 c.249C>G synonymous_variant 0.95 para-aminosalicylic_acid
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
ddn 3987098 c.256_261delCCGATG conservative_inframe_deletion 1.0 pretomanid
delamanid
clpC1 4039517 c.1188C>G synonymous_variant 0.13 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248304 c.1791G>C synonymous_variant 0.14 ethambutol
embB 4248316 c.1803C>G synonymous_variant 0.15 ethambutol
embB 4248319 c.1806A>G synonymous_variant 0.2 ethambutol
ethR 4326904 c.-645G>A upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4408101 c.102G>C synonymous_variant 0.98 streptomycin Not assoc w R - Interim