TB-Profiler result

Run: SRR10123881
Summary

Run ID: SRR10123881

Sample name:

Date: 2024-05-17T14:34:02.496600

Number of reads: 26337330

Percentage reads mapped: 98.7

Median coverage: 870.25

Strain: lineage4.1.4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.4 Euro-American None 1.0
lineage4.1 Euro-American None 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 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778042 p.Ala147Thr missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.1 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.1 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.1 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.31 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3640608 c.-927G>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
rpoA 3877689 c.819C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
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
embB 4246250 c.-264G>T upstream_gene_variant 0.99 ethambutol
embB 4249408 c.2895G>A 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin