TB-Profiler result

Run: ERR4829247
Summary

Run ID: ERR4829247

Sample name:

Date: 01-04-2023 19:22:11

Number of reads: 2521745

Percentage reads mapped: 98.73

Strain: lineage4.3.3

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.98 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289099 p.Lys48Thr missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 1.0 ethionamide
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.15
mshA 576516 p.Val390Ala missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.14
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.14
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.15
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.17
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.17
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.17
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.18
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.18
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.14
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.23
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
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 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243392 p.Asn54Asp missense_variant 1.0
ubiA 4269731 p.Ala35Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407986 p.Gly73Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0