TB-Profiler result

Run: SRR13861326

Summary

Run ID: SRR13861326

Sample name:

Date: 2024-10-04T22:11:26.067138

Number of reads: 2297538

Percentage reads mapped: 57.49

Median coverage: 77.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other


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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 embB p.Arg460Cys Mutation from literature
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
embB 4247891 p.Arg460Cys missense_variant 0.93 ethambutol Mutation from literature
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 6088 c.849C>A synonymous_variant 1.0 levofloxacin
moxifloxacin
hadA 731690 c.-240A>G upstream_gene_variant 1.0 isoniazid
hadA 732094 c.165T>C synonymous_variant 1.0 isoniazid
nusG 734764 p.Ala171Ser missense_variant 0.97 rifampicin
rpoB 760181 c.375T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760328 c.522G>C synonymous_variant 0.13 rifampicin
rpoB 760730 c.924T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761786 c.1980C>T synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoC 763945 c.576T>C synonymous_variant 0.14 rifampicin
rpoC 763960 c.591T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763967 p.Gly200Ser missense_variant 0.13 rifampicin
rpoC 764040 p.Ser224Asn missense_variant 0.13 rifampicin
rpoC 764626 c.1257C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764973 p.Asp535Ala missense_variant 0.93 rifampicin
rpoC 766390 c.3021C>T synonymous_variant 0.13 rifampicin
rpoC 766408 c.3039C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.15 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.14 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.14 rifampicin
rpoC 766484 p.Val1039Ile missense_variant 0.14 rifampicin Uncertain significance
rpoC 766492 c.3123T>C synonymous_variant 0.14 rifampicin
rpoC 766495 c.3126C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766522 c.3153C>G synonymous_variant 0.16 rifampicin
rpoC 766528 c.3159T>C synonymous_variant 0.17 rifampicin
rpoC 766531 c.3162G>T synonymous_variant 0.17 rifampicin
rpoC 766543 c.3174C>T synonymous_variant 0.17 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.18 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.17 rifampicin
rpoC 766583 p.Gly1072Ser missense_variant 0.19 rifampicin
rpoC 766588 c.3219G>A synonymous_variant 0.18 rifampicin
rpoC 766591 c.3222A>G synonymous_variant 0.19 rifampicin
rpoC 766594 c.3225G>C synonymous_variant 0.2 rifampicin
rpoC 766607 p.Ile1080Leu missense_variant 0.17 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.17 rifampicin
rpoC 766645 c.3276A>G synonymous_variant 0.16 rifampicin
rpoC 766651 c.3282T>C synonymous_variant 0.18 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.16 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.15 rifampicin
rpoC 766738 c.3369G>T synonymous_variant 0.12 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.14 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.14 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767009 p.Ser1214Thr missense_variant 0.14 rifampicin
rpoC 767014 c.3645G>C synonymous_variant 0.14 rifampicin
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.14 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.16 rifampicin
rpoC 767074 c.3705T>C synonymous_variant 0.14 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>G synonymous_variant 0.14 rifampicin
rpoC 767158 c.3789T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767167 c.3798C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767180 p.Ala1271Gln missense_variant 0.15 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpsL 781532 c.-28G>T upstream_gene_variant 1.0 streptomycin
rplC 800224 c.-585G>C upstream_gene_variant 1.0 linezolid
fbiC 1302843 c.-88A>C upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1302887 c.-43delG upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
rrl 1473434 n.-224T>C upstream_gene_variant 0.97 capreomycin
linezolid
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476368 n.2711T>A non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rpsA 1833260 c.-282G>C upstream_gene_variant 1.0 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833790 c.249T>A synonymous_variant 0.13 pyrazinamide
rpsA 1833799 c.258C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.13 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>A synonymous_variant 0.14 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.13 pyrazinamide
katG 2156364 c.-253T>G upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2221814 p.Leu451Val missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2222030 p.Val379Met missense_variant 1.0 bedaquiline
clofazimine
kasA 2518687 c.573C>T synonymous_variant 0.13 isoniazid
kasA 2518696 c.582C>G synonymous_variant 0.13 isoniazid
kasA 2518717 c.603C>T synonymous_variant 0.15 isoniazid
kasA 2518723 p.Glu203Asp missense_variant 0.14 isoniazid
kasA 2518732 c.618C>G synonymous_variant 0.15 isoniazid
kasA 2519238 p.Thr375Lys missense_variant 1.0 isoniazid
folC 2747285 p.Val105Ala missense_variant 0.97 para-aminosalicylic_acid
Rv2477c 2783110 c.933C>A synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783116 c.927T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783203 c.840C>T synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783221 c.822G>T synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783243 p.Thr267Ser missense_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783247 c.796T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783254 c.789A>G synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783263 c.780G>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783278 c.765A>G synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783287 c.756C>G synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783290 c.753G>C synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783578 p.Glu155Asp missense_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784556 c.-514A>C upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
pepQ 2859712 p.Thr236Ser missense_variant 1.0 bedaquiline
clofazimine
Rv2681 2996593 c.-146T>C upstream_gene_variant 1.0 capreomycin
Rv2681 2997178 p.Val147Glu missense_variant 1.0 capreomycin
Rv2752c 3065064 c.1128G>T synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyX 3068085 c.-140T>A upstream_gene_variant 0.99 para-aminosalicylic_acid
ald 3087003 p.Asp62His missense_variant 1.0 cycloserine
Rv3083 3448914 p.Ile137Met missense_variant 1.0 ethionamide
whiB7 3568676 p.Ser2Pro missense_variant 1.0 kanamycin
amikacin
streptomycin
mtrB 3625172 p.Thr481Ser missense_variant 1.0 rifampicin
bedaquiline
lpqB 3625687 c.-777G>C upstream_gene_variant 0.13 rifampicin
bedaquiline
lpqB 3625696 c.-786A>G upstream_gene_variant 0.14 rifampicin
bedaquiline
mtrB 3625705 c.909C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625714 c.-804C>T upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3625720 c.894G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625729 c.885A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625735 c.879C>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625750 c.864G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625755 p.Ala287Thr missense_variant 0.16 rifampicin Uncertain significance
bedaquiline
mtrB 3625797 p.Val273Met missense_variant 0.13 rifampicin Uncertain significance
bedaquiline Uncertain significance
fbiA 3641491 p.Ala317Pro missense_variant 1.0 pretomanid
delamanid
clofazimine
alr 3840235 p.Gly396* stop_gained 0.99 cycloserine
alr 3840304 c.1116delT frameshift_variant 0.94 cycloserine
alr 3841263 p.Arg53His missense_variant 1.0 cycloserine
rpoA 3878082 c.426T>C synonymous_variant 0.13 rifampicin
glpK 4139790 c.-35C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.12 ethambutol Not assoc w R
embC 4240706 p.Val282Thr missense_variant 0.13 ethambutol
embC 4240726 c.864G>C synonymous_variant 0.15 ethambutol Not assoc w R - Interim
embC 4240789 c.927T>C synonymous_variant 0.14 ethambutol
embC 4241029 p.Trp389* stop_gained 0.95 ethambutol
embB 4249631 p.Thr1040Pro missense_variant 0.98 ethambutol
ethA 4327197 p.Gly93Arg missense_variant 1.0 ethionamide Uncertain significance