TB-Profiler result

Run: SRR6650168
Summary

Run ID: SRR6650168

Sample name:

Date: 15-08-2023 07:35:15

Number of reads: 474717

Percentage reads mapped: 99.73

Strain: lineage4.3.4.2

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.98
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
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
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
gyrB 5353 c.114T>G synonymous_variant 0.18
gyrB 6645 p.Ser469Asn missense_variant 0.3
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.89
mshA 575886 p.Leu180Arg missense_variant 0.17
mshA 576723 p.Val459Gly missense_variant 0.29
ccsA 619831 c.-60T>G upstream_gene_variant 0.25
ccsA 620138 p.Val83Gly missense_variant 0.2
ccsA 620143 p.Tyr85His missense_variant 0.17
ccsA 620151 c.261C>G synonymous_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775588 c.2893T>G stop_lost&splice_region_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776176 p.Ser769Pro missense_variant 0.22
mmpL5 778239 p.Val81Gly missense_variant 0.2
mmpR5 779318 p.Ala110Glu missense_variant 0.2
mmpR5 779328 p.Glu113Asp missense_variant 0.2
mmpR5 779346 p.Asp119Glu missense_variant 0.36
mmpR5 779348 p.Val120Gly missense_variant 0.46
mmpR5 779354 p.Leu122Arg missense_variant 0.15
mmpR5 779356 p.Arg123Gly missense_variant 0.31
mmpR5 779363 p.Leu125Arg missense_variant 0.33
mmpR5 779369 p.Asp127Ala missense_variant 0.15
mmpR5 779371 p.Ala128Pro missense_variant 0.31
rpsL 781363 c.-197T>G upstream_gene_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801019 p.Thr71Pro missense_variant 0.17
rplC 801274 p.Thr156Pro missense_variant 0.3
rplC 801287 p.Val160Gly missense_variant 0.44
rplC 801297 c.489C>G synonymous_variant 0.22
rplC 801316 p.Met170Val missense_variant 0.3
fbiC 1303016 p.Val29Gly missense_variant 0.38
fbiC 1303021 p.Arg31Gly missense_variant 0.22
fbiC 1304438 p.Glu503Gly missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.33
inhA 1673679 c.-523T>G upstream_gene_variant 0.22
fabG1 1674038 p.Gln200Arg missense_variant 0.33
fabG1 1674065 p.Lys209Arg missense_variant 0.5
fabG1 1674076 p.Thr213Pro missense_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918410 c.471C>T synonymous_variant 0.2
ndh 2103225 c.-183A>C upstream_gene_variant 0.38
ndh 2103227 c.-185T>C upstream_gene_variant 0.25
ndh 2103235 c.-193C>G upstream_gene_variant 0.38
ndh 2103239 c.-197T>G upstream_gene_variant 0.22
PPE35 2168686 p.Thr643Ser missense_variant 0.15
PPE35 2169317 c.1296C>T synonymous_variant 0.33
PPE35 2169820 p.Asn265His missense_variant 0.15
PPE35 2169830 p.Asn261Lys missense_variant 0.17
PPE35 2169854 c.759T>G synonymous_variant 0.36
PPE35 2170082 c.531T>G synonymous_variant 0.33
PPE35 2170390 p.Trp75Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289500 c.-259A>G upstream_gene_variant 0.4
pncA 2289509 c.-268A>G upstream_gene_variant 0.38
pncA 2289511 c.-270T>G upstream_gene_variant 0.57
pncA 2289554 c.-313G>T upstream_gene_variant 0.2
kasA 2518147 c.33C>T synonymous_variant 0.31
kasA 2518151 p.Ser13Arg missense_variant 0.31
kasA 2518161 p.Val16Gly missense_variant 0.25
kasA 2518166 p.Ala18Pro missense_variant 0.18
kasA 2518172 p.Thr20Pro missense_variant 0.2
kasA 2518192 c.78G>C synonymous_variant 0.18
kasA 2518605 p.Val164Gly missense_variant 0.36
eis 2715103 p.Leu77Pro missense_variant 0.18
eis 2715542 c.-210T>G upstream_gene_variant 0.22
folC 2746742 p.Tyr286Phe missense_variant 0.33
folC 2746745 p.Val285Gly missense_variant 0.33
pepQ 2859358 p.Thr354Asn missense_variant 0.17
pepQ 2859377 p.Thr348Ala missense_variant 0.2
pepQ 2859414 c.1005T>G synonymous_variant 0.18
Rv2752c 3064677 p.Glu505Asp missense_variant 0.25
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087888 p.Thr357Pro missense_variant 0.33
fbiD 3339193 p.Leu26Val missense_variant 0.17
fbiD 3339279 c.162T>G synonymous_variant 0.25
fbiD 3339688 p.Thr191Pro missense_variant 0.25
Rv3083 3448484 c.-20T>G upstream_gene_variant 0.18
Rv3083 3449079 p.Leu192Phe missense_variant 0.38
Rv3083 3449089 p.Met196Val missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.18
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612388 c.729T>G synonymous_variant 0.33
Rv3236c 3612835 c.282T>G synonymous_variant 0.22
fbiB 3642740 c.1206C>T synonymous_variant 0.2
fbiB 3642751 p.Asp406Ala missense_variant 0.33
fbiB 3642772 p.Asp413Ala missense_variant 0.3
ddn 3986919 p.Thr26Pro missense_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 0.94
embC 4239973 c.111T>G synonymous_variant 0.36
embC 4240006 c.144A>C synonymous_variant 0.22
embC 4240017 p.Val52Gly missense_variant 0.3
embC 4240050 p.Gln63Pro missense_variant 0.18
embC 4240283 p.Thr141Pro missense_variant 0.14
embC 4240520 p.Thr220Pro missense_variant 0.29
embC 4242387 p.Asn842Thr missense_variant 0.25
embC 4242390 p.Leu843Arg missense_variant 0.29
embC 4242393 p.Asp844Ala missense_variant 0.29
embC 4242398 p.Ala846Pro missense_variant 0.25
embA 4242406 c.-827A>C upstream_gene_variant 0.33
embC 4242408 p.Pro849Arg missense_variant 0.33
embC 4242414 p.Leu851Arg missense_variant 0.33
embC 4242422 p.Trp854Gly missense_variant 0.44
embC 4242425 p.Arg855Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243344 p.Gln38Lys missense_variant 0.22
embA 4243350 p.Thr40Pro missense_variant 0.25
embB 4247616 p.Glu368Gly missense_variant 0.23
embB 4248663 p.Val717Gly missense_variant 0.18
ubiA 4269848 c.-15A>G upstream_gene_variant 0.33
ubiA 4269864 c.-31C>G upstream_gene_variant 0.45
ethA 4326874 p.Lys200Gln missense_variant 0.25
ethR 4326880 c.-669G>C upstream_gene_variant 0.18
ethA 4326887 p.Asp196Gly missense_variant 0.33
ethR 4326898 c.-651C>G upstream_gene_variant 0.17
ethA 4326905 p.Leu190Pro missense_variant 0.25
ethR 4326907 c.-642C>G upstream_gene_variant 0.25
ethR 4327813 p.Thr89Pro missense_variant 0.38
ethA 4327827 c.-354A>G upstream_gene_variant 0.36
ethA 4328218 c.-745A>C upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0