TB-Profiler result

Run: ERR1213930
Summary

Run ID: ERR1213930

Sample name:

Date: 19-10-2023 21:02:45

Number of reads: 4865630

Percentage reads mapped: 92.47

Strain: lineage4.3.2

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.462C>T (0.34)
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 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
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 1472307 n.462C>T non_coding_transcript_exon_variant 0.34 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8619 c.1318T>C synonymous_variant 0.12
gyrA 8627 c.1326C>G synonymous_variant 0.13
gyrA 8636 c.1335A>C synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761636 c.1830G>C synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.89
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776230 c.2251T>C synonymous_variant 0.14
mmpL5 776234 c.2247A>G synonymous_variant 0.12
mmpL5 777455 c.1026G>C synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.33
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.35
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.55
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.3
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.3
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.3
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.46
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.48
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.6
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.29
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.29
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.29
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.29
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.29
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.2
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.21
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.21
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.22
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.35
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.45
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.55
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.48
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.41
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.32
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.26
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.33
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.32
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.34
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.36
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.35
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.23
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.21
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.31
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.33
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.21
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.21
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.21
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.21
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.19
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.39
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.5
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.5
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.38
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.34
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.3
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.3
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.47
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.46
rrl 1476746 n.3089T>A non_coding_transcript_exon_variant 0.31
rrl 1476755 n.3098G>T non_coding_transcript_exon_variant 0.22
rrl 1476759 n.3102T>A non_coding_transcript_exon_variant 0.19
fabG1 1674037 p.Gln200Glu missense_variant 0.17
inhA 1674051 c.-151A>G upstream_gene_variant 0.15
inhA 1674054 c.-148T>C upstream_gene_variant 0.13
inhA 1674060 c.-142A>G upstream_gene_variant 0.16
inhA 1674063 c.-139G>C upstream_gene_variant 0.16
fabG1 1674079 p.Pro214Ala missense_variant 0.19
inhA 1674570 c.369G>C synonymous_variant 0.14
inhA 1674589 p.Met130Leu missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.97
clpC1 4039064 c.1641C>A synonymous_variant 0.21
clpC1 4039079 c.1626C>G synonymous_variant 0.21
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.13
clpC1 4039937 c.768G>C synonymous_variant 0.12
clpC1 4039946 c.759A>C synonymous_variant 0.13
clpC1 4040063 c.642G>C synonymous_variant 0.12
embC 4240853 c.991C>T synonymous_variant 0.13
embC 4242498 p.Arg879Lys missense_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4269372 c.-536G>A upstream_gene_variant 0.14
ubiA 4269380 p.Val152Ile missense_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 0.13
aftB 4269390 c.-554G>C upstream_gene_variant 0.12
aftB 4269402 c.-566T>C upstream_gene_variant 0.14
aftB 4269411 c.-575T>C upstream_gene_variant 0.13
aftB 4269414 c.-578T>C upstream_gene_variant 0.13
aftB 4269420 c.-584T>C upstream_gene_variant 0.12
ubiA 4269424 p.Ala137Gly missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0