TB-Profiler result

Run: SRR13861266

Summary

Run ID: SRR13861266

Sample name:

Date: 2024-03-26T12:24:39.010821

Number of reads: 2713157

Percentage reads mapped: 45.26

Median coverage: 90.0

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) 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
gyrB 5540 p.Thr101Ser missense_variant 1.0 levofloxacin
moxifloxacin
gyrB 6223 c.984G>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6242 p.Arg335Lys missense_variant 0.16 levofloxacin
moxifloxacin
gyrB 6250 c.1011A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6253 c.1014G>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrB 6280 c.1041T>C synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrB 6286 c.1047T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrB 6292 c.1053G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrB 6295 c.1056A>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrB 6298 c.1059C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6299 c.1060C>T synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrB 6307 c.1068T>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6325 c.-977C>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6361 c.-941G>A upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 7626 c.325C>T synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7631 c.330G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7637 c.336C>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7649 c.348C>T synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 7652 c.351C>T synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7658 c.357A>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7664 c.363T>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 7670 c.369A>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 7683 c.382A>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7697 c.396C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 7710 c.409T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7715 c.414G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7730 p.Arg143Ser missense_variant 0.14 levofloxacin
moxifloxacin
nusG 734249 c.-5A>G upstream_gene_variant 1.0 rifampicin
nusG 734917 p.Phe222Leu missense_variant 0.98 rifampicin
rpoB 760558 c.753delC frameshift_variant 0.95 rifampicin
rpoB 760611 p.Leu269Val missense_variant 1.0 rifampicin
rpoB 762490 p.Val895Gly missense_variant 1.0 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.13 rifampicin
rpoC 763768 c.399C>G synonymous_variant 0.14 rifampicin
rpoC 763780 c.411C>G synonymous_variant 0.13 rifampicin
rpoC 765707 c.2340delA frameshift_variant 0.93 rifampicin
Rv1129c 1253076 c.1459T>G stop_lost&splice_region_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674561 c.360C>T synonymous_variant 0.12 ethionamide
isoniazid
tsnR 1854059 p.Leu152Val missense_variant 1.0 linezolid
ndh 2101690 p.Glu451Asp missense_variant 1.0 ethionamide
delamanid
isoniazid
PPE35 2168961 p.Gly551Val missense_variant 1.0 pyrazinamide
PPE35 2170927 c.-315A>G upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2222084 p.Leu361Ile missense_variant 1.0 clofazimine
bedaquiline
Rv1979c 2222431 p.Met245Arg missense_variant 1.0 clofazimine
bedaquiline
Rv1979c 2223625 c.-461C>A upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ald 3087020 c.201C>T synonymous_variant 1.0 cycloserine
mtrB 3625191 p.Val475Leu missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625358 p.Asn419Thr missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625682 p.Leu311Gln missense_variant 0.95 bedaquiline
rifampicin
alr 3841157 c.264A>G synonymous_variant 1.0 cycloserine
rpoA 3878047 p.Ala154Asp missense_variant 0.97 rifampicin
clpC1 4040426 c.279T>C synonymous_variant 0.14 pyrazinamide
embB 4247452 c.939C>T synonymous_variant 0.93 ethambutol
ethR 4326799 c.-750G>A upstream_gene_variant 1.0 ethionamide