TB-Profiler result

Run: ERR182026
Summary

Run ID: ERR182026

Sample name:

Date: 20-10-2023 22:41:06

Number of reads: 3370130

Percentage reads mapped: 99.32

Strain: lineage4.1.2;lineage1.1.3.2

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 0.14
lineage1 Indo-Oceanic EAI RD239 0.86
lineage4.1 Euro-American T;X;H None 0.1
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.85
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.85
lineage4.1.2 Euro-American T;H None 0.15
lineage1.1.3.2 Indo-Oceanic NA RD239 0.84
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 6112 p.Met291Ile missense_variant 0.86
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 0.84
gyrA 8452 p.Ala384Val missense_variant 0.88
gyrA 9143 c.1842T>C synonymous_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 0.84
ccsA 619695 c.-196G>A upstream_gene_variant 0.81
rpoC 763031 c.-339T>C upstream_gene_variant 0.79
rpoC 763884 p.Ala172Val missense_variant 0.83
rpoC 763886 c.517C>A synonymous_variant 0.84
rpoC 765150 p.Gly594Glu missense_variant 0.19
rpoC 765171 p.Pro601Leu missense_variant 0.83
rpoC 765230 p.Ala621Thr missense_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.81
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 0.83
Rv1258c 1407055 c.285delG frameshift_variant 0.81
embR 1417019 p.Cys110Tyr missense_variant 0.81
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673249 c.-191C>T upstream_gene_variant 0.13
inhA 1674883 p.Ile228Val missense_variant 0.79
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.75
PPE35 2167926 p.Leu896Ser missense_variant 0.89
PPE35 2167983 p.Gly877Asp missense_variant 0.9
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.82
ahpC 2726051 c.-142G>A upstream_gene_variant 0.9
folC 2747022 p.Val193Ile missense_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 0.76
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.88
Rv3083 3448894 p.Tyr131Asp missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.86
fprA 3475159 p.Asn385Asp missense_variant 0.87
fbiA 3641164 p.Ile208Val missense_variant 0.14
fbiB 3642173 c.639G>A synonymous_variant 0.86
rpoA 3878687 c.-180A>C upstream_gene_variant 0.85
clpC1 4040517 p.Val63Ala missense_variant 0.88
embC 4240671 p.Thr270Ile missense_variant 0.86
embC 4241042 p.Asn394Asp missense_variant 0.8
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.89
embA 4244255 c.1023T>G synonymous_variant 0.84
embA 4245025 p.His598Arg missense_variant 0.82
embA 4245969 p.Pro913Ser missense_variant 0.72
embB 4247646 p.Glu378Ala missense_variant 0.84
aftB 4268861 c.-25T>C upstream_gene_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.83
aftB 4269606 c.-770T>C upstream_gene_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.86
gid 4407588 c.615A>G synonymous_variant 0.86
gid 4407661 p.Ser181Leu missense_variant 0.88
gid 4407780 c.423G>A synonymous_variant 0.87
gid 4407873 c.330G>T synonymous_variant 0.83