TB-Profiler result

Run: ERR4814802
Summary

Run ID: ERR4814802

Sample name:

Date: 20-10-2023 07:39:12

Number of reads: 2681098

Percentage reads mapped: 99.34

Strain: lineage4.1.2;lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 0.74
lineage4.1 Euro-American T;X;H None 0.24
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.78
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.75
lineage4.1.2 Euro-American T;H None 0.21
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 0.85
gyrB 6124 c.885C>T synonymous_variant 0.84
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.71
gyrA 9143 c.1842T>C synonymous_variant 0.78
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.31
fgd1 491742 c.960T>C synonymous_variant 0.8
rpoB 760115 c.309C>T synonymous_variant 0.28
rpoB 761069 c.1263C>T synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.82
rpoC 763884 p.Ala172Val missense_variant 0.75
rpoC 763886 c.517C>A synonymous_variant 0.73
rpoC 764263 c.894G>A synonymous_variant 0.28
rpoC 765150 p.Gly594Glu missense_variant 0.24
rpoC 765171 p.Pro601Leu missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 777320 c.1161C>G synonymous_variant 0.23
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416290 p.Gln353Pro missense_variant 0.8
embR 1417019 p.Cys110Tyr missense_variant 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833904 p.Glu121Asp missense_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918584 c.645A>C synonymous_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 0.8
PPE35 2167926 p.Leu896Ser missense_variant 0.87
PPE35 2167983 p.Gly877Asp missense_variant 0.73
Rv1979c 2222308 p.Asp286Gly missense_variant 0.64
Rv1979c 2222641 p.Ser175Leu missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 0.73
ahpC 2726051 c.-142G>A upstream_gene_variant 0.7
folC 2746488 p.Asp371Tyr missense_variant 0.88
Rv2752c 3064632 c.1560C>T synonymous_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339059 c.-58delC upstream_gene_variant 0.72
Rv3083 3448714 p.Asp71His missense_variant 0.86
Rv3083 3449959 p.Ala486Ser missense_variant 0.73
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.77
fprA 3475159 p.Asn385Asp missense_variant 0.78
Rv3236c 3611974 c.1143A>C synonymous_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 0.81
embC 4240671 p.Thr270Ile missense_variant 0.81
embC 4241042 p.Asn394Asp missense_variant 0.77
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.24
embA 4243848 p.Val206Met missense_variant 0.77
embA 4244148 p.Trp306Arg missense_variant 0.72
embA 4245969 p.Pro913Ser missense_variant 0.82
embB 4247646 p.Glu378Ala missense_variant 0.7
embB 4248365 p.Val618Met missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 0.78
aftB 4269606 c.-770T>C upstream_gene_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.73
gid 4407588 c.615A>G synonymous_variant 0.79
gid 4407873 c.330G>T synonymous_variant 0.81