TB-Profiler result

Run: ERR1035091
Summary

Run ID: ERR1035091

Sample name:

Date: 20-10-2023 23:53:44

Number of reads: 4789271

Percentage reads mapped: 99.34

Strain: lineage4.8;lineage1.1.1

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 gid c.115delC (0.38)
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 0.65
lineage1 Indo-Oceanic EAI RD239 0.33
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.38
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.66
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.32
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
gid 4408087 c.115delC frameshift_variant 0.38 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 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.38
gyrA 8452 p.Ala384Val missense_variant 0.4
gyrA 9143 c.1842T>C synonymous_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 0.42
rpoC 763031 c.-339T>C upstream_gene_variant 0.37
rpoC 763884 p.Ala172Val missense_variant 0.26
rpoC 763886 c.517C>A synonymous_variant 0.27
rpoC 765171 p.Pro601Leu missense_variant 0.39
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.34
mmpL5 777804 p.Ile226Thr missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.36
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.52
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.38
rpsA 1834319 p.Val260Ile missense_variant 0.45
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102809 p.Lys78Asn missense_variant 0.65
katG 2154724 p.Arg463Leu missense_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 0.41
PPE35 2167983 p.Gly877Asp missense_variant 0.39
Rv1979c 2222308 p.Asp286Gly missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289414 c.-173A>G upstream_gene_variant 0.6
kasA 2518132 c.18C>T synonymous_variant 0.32
ahpC 2726051 c.-142G>A upstream_gene_variant 0.34
Rv2752c 3064632 c.1560C>T synonymous_variant 0.41
ald 3086788 c.-32T>C upstream_gene_variant 0.35
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.32
fprA 3474597 c.591C>A synonymous_variant 0.35
fprA 3475159 p.Asn385Asp missense_variant 0.35
fbiB 3641064 c.-471G>A upstream_gene_variant 0.41
alr 3840280 p.Asp381Asn missense_variant 0.36
clpC1 4040517 p.Val63Ala missense_variant 0.38
embC 4240671 p.Thr270Ile missense_variant 0.32
embC 4241042 p.Asn394Asp missense_variant 0.32
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.3
embA 4244096 c.864C>T synonymous_variant 0.24
embA 4245969 p.Pro913Ser missense_variant 0.37
embB 4247646 p.Glu378Ala missense_variant 0.33
aftB 4268051 c.786G>A synonymous_variant 0.4
ubiA 4269387 p.Glu149Asp missense_variant 0.32
aftB 4269606 c.-770T>C upstream_gene_variant 0.32
whiB6 4338242 p.Gln94Glu missense_variant 0.37
whiB6 4338400 p.Trp41Leu missense_variant 0.59
whiB6 4338595 c.-75delG upstream_gene_variant 0.61
whiB6 4338603 c.-82C>T upstream_gene_variant 0.4
whiB6 4338605 c.-84C>G upstream_gene_variant 0.61
gid 4407588 c.615A>G synonymous_variant 0.46
gid 4407873 c.330G>T synonymous_variant 0.41