TB-Profiler result

Run: ERR4407450
Summary

Run ID: ERR4407450

Sample name:

Date: 01-04-2023 05:44:34

Number of reads: 253338

Percentage reads mapped: 86.37

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
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 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
pncA 2288703 p.Val180Ala missense_variant 0.29 pyrazinamide
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 7946 c.645C>T synonymous_variant 0.14
gyrA 8553 c.1255delG frameshift_variant 0.11
gyrA 8877 p.Ala526Thr missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762353 c.2547C>A synonymous_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778061 p.Gln140His missense_variant 1.0
mmpS5 778491 p.Val139Met missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.3
Rv1258c 1406107 p.Asp412His missense_variant 0.17
atpE 1460872 c.-173G>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472096 n.251T>G non_coding_transcript_exon_variant 0.25
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.1
rrl 1475673 n.2020_2021delAA non_coding_transcript_exon_variant 0.17
rrl 1476213 n.2556G>A non_coding_transcript_exon_variant 0.11
inhA 1674184 c.-18C>A upstream_gene_variant 0.13
rpsA 1834648 c.1107C>T synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223317 c.-153C>T upstream_gene_variant 0.13
pncA 2289084 p.Asp53Gly missense_variant 0.29
folC 2747657 c.-59C>T upstream_gene_variant 0.22
pepQ 2860537 c.-119C>A upstream_gene_variant 0.11
ribD 2987128 p.Arg97Gln missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448587 c.84C>T synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038856 p.Lys617* stop_gained 0.13
embC 4242321 p.Pro820Leu missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246409 c.3178delT frameshift_variant 0.13
aftB 4268880 c.-44C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408096 c.106delG frameshift_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0