TB-Profiler result

Run: SRR22251865
Summary

Run ID: SRR22251865

Sample name:

Date: 10-02-2024 17:12:01

Number of reads: 1771870

Percentage reads mapped: 99.6

Strain: lineage4.5;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 0.68
lineage1 Indo-Oceanic EAI RD239 0.37
lineage4.5 Euro-American H;T RD122 0.62
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.3
lineage1.2.1.2 Indo-Oceanic NA RD239 0.33
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.33
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 0.39
gyrA 7362 p.Glu21Gln missense_variant 0.98
gyrA 7585 p.Ser95Thr missense_variant 0.98
gyrA 7892 c.591G>A synonymous_variant 0.49
gyrA 8452 p.Ala384Val missense_variant 0.46
gyrA 9143 c.1842T>C synonymous_variant 0.34
gyrA 9260 c.1959G>C synonymous_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575368 c.21T>C synonymous_variant 0.31
ccsA 620029 c.139C>T synonymous_variant 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 0.26
rpoC 763531 c.162G>C synonymous_variant 0.41
rpoC 763884 p.Ala172Val missense_variant 0.4
rpoC 763886 c.517C>A synonymous_variant 0.4
rpoC 766876 p.Asp1169Glu missense_variant 0.78
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 0.72
Rv1258c 1406312 c.1029T>C synonymous_variant 0.23
embR 1417019 p.Cys110Tyr missense_variant 0.39
atpE 1460907 c.-138T>C upstream_gene_variant 0.54
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834930 c.1389A>C synonymous_variant 0.61
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 0.41
PPE35 2170568 p.Ile15Met missense_variant 0.58
Rv1979c 2222308 p.Asp286Gly missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288746 p.Asp166Asn missense_variant 0.55
kasA 2518132 c.18C>T synonymous_variant 0.38
kasA 2519048 p.Gly312Ser missense_variant 0.27
ahpC 2726051 c.-142G>A upstream_gene_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 0.37
fbiD 3339417 c.300A>G synonymous_variant 0.32
Rv3083 3448714 p.Asp71His missense_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.38
fprA 3475159 p.Asn385Asp missense_variant 0.24
whiB7 3568488 c.191delG frameshift_variant 0.4
clpC1 4038318 p.Pro796Leu missense_variant 0.59
clpC1 4040517 p.Val63Ala missense_variant 0.44
embC 4240671 p.Thr270Ile missense_variant 0.32
embC 4241042 p.Asn394Asp missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 0.34
embA 4244420 c.1188G>C synonymous_variant 0.36
embA 4245969 p.Pro913Ser missense_variant 0.36
embB 4247028 p.Leu172Arg missense_variant 0.22
embB 4247578 c.1065G>A synonymous_variant 0.44
embB 4247646 p.Glu378Ala missense_variant 0.3
ubiA 4269387 p.Glu149Asp missense_variant 0.43
aftB 4269606 c.-770T>C upstream_gene_variant 0.43
ubiA 4269864 c.-32delG upstream_gene_variant 0.41
ethA 4327205 p.Ala90Val missense_variant 0.55
whiB6 4338218 p.Asn102Asp missense_variant 0.58
whiB6 4338361 p.Arg54Gln missense_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.42
gid 4407588 c.615A>G synonymous_variant 0.49
gid 4407873 c.330G>T synonymous_variant 0.23