TB-Profiler result

Run: ERR11082919
Summary

Run ID: ERR11082919

Sample name:

Date: 11-04-2023 12:16:51

Number of reads: 721977

Percentage reads mapped: 99.56

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 1.0
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8414 c.1113C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619817 c.-74C>T upstream_gene_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759989 c.183G>T synonymous_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779131 p.Pro48Ala missense_variant 0.14
mmpL5 779196 c.-716G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305376 p.Ile816Phe missense_variant 0.11
embR 1416448 c.900C>G synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476330 n.2673A>G non_coding_transcript_exon_variant 0.11
rpsA 1834076 p.Asn179Tyr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102247 p.Val266Ile missense_variant 0.17
ndh 2102282 p.Arg254His missense_variant 0.11
ndh 2102614 c.429C>T synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167764 p.Ile950Thr missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169944 c.669G>A synonymous_variant 0.11
PPE35 2170065 p.Ala183Gly missense_variant 0.23
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97
folC 2746156 c.1442delT frameshift_variant 0.12
ribD 2987260 c.424delG frameshift_variant 0.2
Rv2752c 3065439 c.753C>A synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339085 c.-33T>C upstream_gene_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.36
Rv3236c 3612169 c.947delA frameshift_variant 0.12
Rv3236c 3612501 c.614_615delAT frameshift_variant 0.12
fbiA 3641254 p.Ala238Thr missense_variant 0.11
fbiA 3641261 p.Ile240Thr missense_variant 0.11
rpoA 3878613 c.-106A>C upstream_gene_variant 0.4
clpC1 4038190 p.Ser839Arg missense_variant 0.18
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240638 p.His259Arg missense_variant 0.11
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243970 c.738C>T synonymous_variant 0.11
embA 4244496 p.Ala422Thr missense_variant 0.11
embB 4248324 p.Ala604Gly missense_variant 0.29
aftB 4267700 p.Trp379* stop_gained 0.15
aftB 4268823 p.Ser5Asn missense_variant 0.11
ubiA 4269238 p.Ala199Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407993 p.Ser70Arg missense_variant 1.0