TB-Profiler result

Run: ERR9786619
Summary

Run ID: ERR9786619

Sample name:

Date: 2024-10-05T06:10:44.689619

Number of reads: 5787540

Percentage reads mapped: 91.32

Median coverage: 269.0

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 0.97
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 0.98 isoniazid Not assoc w R
gyrB 7017 p.Ala593Val missense_variant 0.91 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7661 c.360C>T synonymous_variant 0.13 levofloxacin
moxifloxacin
Rv0565c 656661 c.810T>C synonymous_variant 0.98 ethionamide
rpoC 764497 c.1128A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.15 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764554 c.1185C>T synonymous_variant 0.15 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764576 p.Ser403Thr missense_variant 0.13 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.16 rifampicin
rpoC 764618 c.1249C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 765796 c.2427C>T synonymous_variant 0.14 rifampicin
rpoC 765835 c.2466C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765886 c.2517C>G synonymous_variant 0.16 rifampicin
rpoC 765928 c.2559C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765994 c.2625A>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766085 p.Pro906Ala missense_variant 0.98 rifampicin Not assoc w R
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
atpE 1460992 c.-53A>C upstream_gene_variant 0.99 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473966 n.309T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1473971 n.314G>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1473981 n.324delGinsTT non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.98 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474036 n.379G>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475201 n.1544G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834528 c.987T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834531 c.990C>T synonymous_variant 0.14 pyrazinamide
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 0.98 ethionamide Uncertain significance
whiB7 3568503 c.177G>T synonymous_variant 0.98 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
alr 3840764 c.657G>C synonymous_variant 0.99 cycloserine
rpoA 3878247 c.261G>C synonymous_variant 0.14 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878276 c.232C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.17 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>T synonymous_variant 0.15 rifampicin
rpoA 3878307 c.201C>G synonymous_variant 0.15 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.15 rifampicin
rpoA 3878716 c.-209C>G upstream_gene_variant 0.15 rifampicin
rpoA 3878725 c.-218A>G upstream_gene_variant 0.14 rifampicin
rpoA 3878742 c.-235G>A upstream_gene_variant 0.13 rifampicin
rpoA 3878749 c.-242G>T upstream_gene_variant 0.14 rifampicin
rpoA 3878761 c.-254G>C upstream_gene_variant 0.15 rifampicin
rpoA 3878785 c.-278T>A upstream_gene_variant 0.15 rifampicin
rpoA 3878788 c.-281G>C upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3878806 c.-299C>G upstream_gene_variant 0.15 rifampicin
rpoA 3878809 c.-302T>C upstream_gene_variant 0.15 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.13 rifampicin
clpC1 4038914 c.1791G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038917 c.1788C>T synonymous_variant 0.13 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.14 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038989 c.1716T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039556 c.1149G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039559 c.1146C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039574 p.Ala377Gly missense_variant 0.15 pyrazinamide
clpC1 4039577 c.1128T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4039592 c.1113G>T synonymous_variant 0.16 pyrazinamide
clpC1 4039610 c.1095G>T synonymous_variant 0.17 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.14 pyrazinamide
glpK 4139183 c.572dupG frameshift_variant 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249511 p.Met1000Leu missense_variant 0.97 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R