TB-Profiler result

Run: ERR12328154
Summary

Run ID: ERR12328154

Sample name:

Date: 12-03-2024 15:58:32

Number of reads: 2525915

Percentage reads mapped: 99.58

Strain: lineage4.2.2;lineage2.2.1;lineage1.1.1.1

Drug-resistance: Other

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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 R rrs n.517C>T (0.79)
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
lineage2 East-Asian Beijing RD105 0.74
lineage4 Euro-American LAM;T;S;X;H None 0.19
lineage1 Indo-Oceanic EAI RD239 0.12
lineage4.2 Euro-American H;T;LAM None 0.16
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.11
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.66
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.17
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.71
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.13
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.1
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.79 streptomycin
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 0.15
gyrA 6961 c.-341G>A upstream_gene_variant 0.79
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9026 c.1725G>A synonymous_variant 0.18
gyrA 9143 c.1842T>C synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.73
mshA 575907 p.Ala187Val missense_variant 0.71
mshA 576077 c.730C>T synonymous_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 0.79
rpoC 765157 c.1788C>T synonymous_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 776182 p.Asp767Asn missense_variant 0.68
mmpL5 777394 c.1087C>A synonymous_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304962 p.Trp678Gly missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7
rrs 1471647 n.-199G>C upstream_gene_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.82
PPE35 2167926 p.Leu896Ser missense_variant 0.89
PPE35 2167983 p.Gly877Asp missense_variant 0.21
Rv1979c 2222308 p.Asp286Gly missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289463 c.-222C>G upstream_gene_variant 0.16
kasA 2518132 c.18C>T synonymous_variant 0.18
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.2
Rv3236c 3612469 c.648A>G synonymous_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 0.7
alr 3841472 c.-52C>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.67
embA 4243848 p.Val206Met missense_variant 0.17
embA 4245969 p.Pro913Ser missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 0.53
ubiA 4269387 p.Glu149Asp missense_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 0.14
ethA 4328331 c.-858C>T upstream_gene_variant 0.14
whiB6 4338296 p.Trp76Arg missense_variant 0.76
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.84
gid 4407927 p.Glu92Asp missense_variant 0.78