TB-Profiler result

Run: ERR11243473
Summary

Run ID: ERR11243473

Sample name:

Date: 21-04-2023 18:45:47

Number of reads: 1919604

Percentage reads mapped: 99.83

Strain: lineage4.8

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 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 7485 c.186delC frameshift_variant 0.29
gyrA 8627 c.1326C>A synonymous_variant 0.13
fgd1 490935 c.153C>T synonymous_variant 0.11
mshA 575583 p.Leu79Gln missense_variant 0.12
ccsA 619989 c.99G>T synonymous_variant 0.18
ccsA 620441 p.Gly184Val missense_variant 0.11
rpoB 761247 p.Glu481* stop_gained 0.12
rpoB 762511 p.Ala902Asp missense_variant 0.15
rpoC 765558 p.Thr730Met missense_variant 0.13
rpoC 767248 p.Tyr1293* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777682 p.Val267Met missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303106 p.Cys59Tyr missense_variant 1.0
fbiC 1304904 p.Glu658Asp missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472536 n.691G>A non_coding_transcript_exon_variant 0.5
rrs 1472815 n.970A>G non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475075 n.1418A>G non_coding_transcript_exon_variant 0.25
rrl 1476264 n.2607A>C non_coding_transcript_exon_variant 0.1
rrl 1476296 n.2639C>A non_coding_transcript_exon_variant 0.13
inhA 1674984 p.Asp261Glu missense_variant 0.2
tlyA 1917741 c.-199T>A upstream_gene_variant 0.11
tlyA 1917761 c.-179C>T upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918498 p.Val187Leu missense_variant 0.1
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289398 c.-157G>T upstream_gene_variant 0.12
kasA 2518147 c.33C>T synonymous_variant 0.19
folC 2746534 c.1065T>C synonymous_variant 0.17
folC 2747106 p.Asp165Tyr missense_variant 0.15
Rv2752c 3064707 c.1485G>T synonymous_variant 0.11
Rv2752c 3065650 p.Arg181His missense_variant 0.15
fprA 3474952 p.Gln316* stop_gained 0.33
fprA 3475066 p.Glu354Gln missense_variant 0.12
fbiB 3640971 c.-564G>T upstream_gene_variant 0.11
fbiB 3641520 c.-15T>G upstream_gene_variant 0.1
fbiB 3641827 p.Arg98Leu missense_variant 0.14
fbiB 3642591 p.Val353Leu missense_variant 0.25
clpC1 4040017 p.Ala230Thr missense_variant 0.12
clpC1 4040112 p.Glu198Gly missense_variant 0.13
embC 4240538 p.Pro226Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243209 c.-24C>G upstream_gene_variant 0.11
embA 4244267 c.1035G>T synonymous_variant 0.17
embA 4245180 p.Phe650Leu missense_variant 0.12
embB 4248785 p.Asp758Tyr missense_variant 0.11
embB 4249210 c.2697G>T synonymous_variant 0.11
embB 4249288 p.Gln925His missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408020 c.183C>A synonymous_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0