TB-Profiler result

Run: ERR212101

Summary

Run ID: ERR212101

Sample name:

Date: 20-10-2023 22:48:40

Number of reads: 6498577

Percentage reads mapped: 96.8

Strain: lineage4.1.1.3

Drug-resistance: Sensitive


Download CSV Download TXT Download PDF Download JSON
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 0.86
lineage4.1 Euro-American T;X;H None 0.86
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.05
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.86
lineage1.2.2.1 Indo-Oceanic NA RD239 0.09
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.86
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 8452 p.Ala384Val missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760898 c.1092C>T synonymous_variant 0.86
rpoC 763031 c.-339T>C upstream_gene_variant 0.13
rpoC 763884 p.Ala172Val missense_variant 0.13
rpoC 763886 c.517C>A synonymous_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.13
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.15
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.12
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.18
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.25
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.23
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.23
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.13
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726753 c.561T>G synonymous_variant 0.88
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.13
rpoA 3878243 p.Glu89Gln missense_variant 0.84
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.86
embB 4249408 c.2895G>A synonymous_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.13
gid 4407989 p.Ala72Ser missense_variant 0.81