TB-Profiler result

Run: ERR2706927
Summary

Run ID: ERR2706927

Sample name:

Date: 19-10-2023 11:59:06

Number of reads: 4616315

Percentage reads mapped: 99.58

Strain: lineage4.7;lineage1.1.3.1

Drug-resistance: RR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Gln432Pro (0.65), rpoB p.Ile480Val (0.66)
Isoniazid
Ethambutol R embB p.Gly406Asp (0.64)
Pyrazinamide R pncA c.387delT (0.15), pncA p.Leu4Ser (0.53)
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 0.63
lineage1 Indo-Oceanic EAI RD239 0.36
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.34
lineage4.7 Euro-American (mainly T) T1;T5 None 0.63
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.36
lineage1.1.3.1 Indo-Oceanic NA RD239 0.37
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
rpoB 761101 p.Gln432Pro missense_variant 0.65 rifampicin
rpoB 761244 p.Ile480Val missense_variant 0.66 rifampicin
pncA 2288854 c.387delT frameshift_variant 0.15 pyrazinamide
pncA 2289231 p.Leu4Ser missense_variant 0.53 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 0.64 ethambutol
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 5731 c.492C>T synonymous_variant 0.41
gyrB 6112 p.Met291Ile missense_variant 0.38
gyrB 6798 p.Gly520Ala missense_variant 0.62
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.38
gyrA 8452 p.Ala384Val missense_variant 0.43
gyrA 9143 c.1842T>C synonymous_variant 0.37
gyrA 9304 p.Gly668Asp missense_variant 0.32
fgd1 491742 c.960T>C synonymous_variant 0.31
mshA 575578 c.231G>C synonymous_variant 0.65
rpoB 761823 p.Asn673His missense_variant 0.68
rpoC 763031 c.-339T>C upstream_gene_variant 0.41
rpoC 763884 p.Ala172Val missense_variant 0.34
rpoC 763886 c.517C>A synonymous_variant 0.34
rpoC 765171 p.Pro601Leu missense_variant 0.33
rpoC 765230 p.Ala621Thr missense_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.35
mmpL5 777628 p.Tyr285His missense_variant 0.36
mmpS5 779526 c.-621G>A upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.37
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.71
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.43
katG 2155213 p.Trp300Ser missense_variant 0.59
PPE35 2167926 p.Leu896Ser missense_variant 0.31
PPE35 2167983 p.Gly877Asp missense_variant 0.32
PPE35 2169104 p.Leu503Phe missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.42
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26
ribD 2987276 c.438G>C synonymous_variant 0.31
Rv2752c 3064632 c.1560C>T synonymous_variant 0.48
ald 3086788 c.-32T>C upstream_gene_variant 0.36
Rv3083 3448714 p.Asp71His missense_variant 0.36
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.31
fprA 3474597 c.591C>A synonymous_variant 0.28
fprA 3475159 p.Asn385Asp missense_variant 0.35
alr 3841253 c.168C>T synonymous_variant 0.3
clpC1 4040517 p.Val63Ala missense_variant 0.39
clpC1 4040770 c.-66C>T upstream_gene_variant 0.41
embC 4240671 p.Thr270Ile missense_variant 0.33
embC 4241042 p.Asn394Asp missense_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.39
embA 4245969 p.Pro913Ser missense_variant 0.34
embB 4247646 p.Glu378Ala missense_variant 0.3
embB 4248161 c.1648C>T synonymous_variant 0.36
embB 4249732 c.3219C>G synonymous_variant 0.83
aftB 4267992 p.Thr282Met missense_variant 0.64
ubiA 4269387 p.Glu149Asp missense_variant 0.39
aftB 4269606 c.-770T>C upstream_gene_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.34
gid 4407780 c.423G>A synonymous_variant 0.26
gid 4407873 c.330G>T synonymous_variant 0.32
gid 4407993 p.Ser70Arg missense_variant 0.72