TB-Profiler result

Run: SRR10808722
Summary

Run ID: SRR10808722

Sample name:

Date: 2024-03-27T01:35:42.661092

Number of reads: 4163830

Percentage reads mapped: 90.1

Median coverage: 133.0

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
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
dnaA 1323 c.1323C>G synonymous_variant 1.0 isoniazid
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
atpE 1461028 c.-17T>C upstream_gene_variant 1.0 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.1 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472954 n.1109T>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472992 n.1147A>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474804 n.1147C>T 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 1474827 n.1170C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476229 n.2572C>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.11 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 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
embC 4242257 p.Val799Met missense_variant 1.0 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R