TB-Profiler result

Run: ERR171164
Summary

Run ID: ERR171164

Sample name:

Date: 20-10-2023 22:08:36

Number of reads: 2085809

Percentage reads mapped: 99.43

Strain: lineage4.4.2;lineage1.2.1.2.1

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 0.72
lineage1 Indo-Oceanic EAI RD239 0.28
lineage4.4 Euro-American S;T None 0.74
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.26
lineage4.4.2 Euro-American T1;T2 None 0.73
lineage1.2.1.2 Indo-Oceanic NA RD239 0.31
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.3
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 0.34
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.36
gyrA 9260 c.1959G>C synonymous_variant 0.32
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491377 p.Gly199Arg missense_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 0.38
mshA 575368 c.21T>C synonymous_variant 0.24
rpoC 763031 c.-339T>C upstream_gene_variant 0.51
rpoC 763531 c.162G>C synonymous_variant 0.38
rpoC 763884 p.Ala172Val missense_variant 0.37
rpoC 763886 c.517C>A synonymous_variant 0.35
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407363 c.-23C>T upstream_gene_variant 0.39
embR 1417019 p.Cys110Tyr missense_variant 0.43
atpE 1460907 c.-138T>C upstream_gene_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674162 c.-40C>T upstream_gene_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 0.32
Rv1979c 2222308 p.Asp286Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289524 c.-283C>T upstream_gene_variant 0.32
kasA 2518132 c.18C>T synonymous_variant 0.39
kasA 2519048 p.Gly312Ser missense_variant 0.26
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26
Rv2752c 3066099 p.Met31Ile missense_variant 0.73
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 0.39
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.3
fprA 3475159 p.Asn385Asp missense_variant 0.24
whiB7 3568488 c.191delG frameshift_variant 0.29
fbiB 3640557 c.-978T>C upstream_gene_variant 0.2
ddn 3987175 p.Ala111Val missense_variant 0.76
clpC1 4040517 p.Val63Ala missense_variant 0.23
embC 4240671 p.Thr270Ile missense_variant 0.3
embC 4241042 p.Asn394Asp missense_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 0.3
embA 4244420 c.1188G>C synonymous_variant 0.24
embB 4246508 c.-6G>A upstream_gene_variant 0.77
embB 4247646 p.Glu378Ala missense_variant 0.4
aftB 4268928 c.-92C>T upstream_gene_variant 0.53
aftB 4269375 c.-539G>A upstream_gene_variant 0.6
ubiA 4269387 p.Glu149Asp missense_variant 0.44
aftB 4269606 c.-770T>C upstream_gene_variant 0.32
ubiA 4269864 c.-32delG upstream_gene_variant 0.36
ethA 4328200 c.-727C>T upstream_gene_variant 0.53
whiB6 4338361 p.Arg54Gln missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.27
gid 4407588 c.615A>G synonymous_variant 0.25
gid 4407873 c.330G>T synonymous_variant 0.24
gid 4408133 p.Glu24* stop_gained 0.29