TB-Profiler result

Run: SRR19241806
Summary

Run ID: SRR19241806

Sample name:

Date: 2024-10-05T10:24:38.260630

Number of reads: 4454534

Percentage reads mapped: 88.32

Median coverage: 147.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American 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
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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.99 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 1.0 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 781276 c.-284A>C upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.1 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.17 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.1 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid Uncertain significance
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476534 n.2878_2879delGG non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
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
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.18 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.23 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239279 c.-584G>A upstream_gene_variant 1.0 ethambutol
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin