TB-Profiler result

Run: ERR025449
Summary

Run ID: ERR025449

Sample name:

Date: 31-03-2023 08:17:18

Number of reads: 664167

Percentage reads mapped: 99.37

Strain: lineage4.3

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
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 0.88
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 6817 c.-485G>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8715 p.Pro472Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 0.89
fgd1 490696 c.-87T>G upstream_gene_variant 0.2
mshA 576468 p.Val374Gly missense_variant 0.67
ccsA 620298 c.408G>T synonymous_variant 0.17
rpoB 762249 p.Leu815Val missense_variant 0.12
rpoC 762836 c.-534C>G upstream_gene_variant 0.3
rpoC 764995 c.1626C>G synonymous_variant 0.68
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781859 c.300T>C synonymous_variant 0.15
atpE 1461019 c.-26C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.83
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.15
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.33
fabG1 1673449 p.Thr4Pro missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918058 p.Val40Gly missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289115 p.His43Tyr missense_variant 0.36
Rv2752c 3065618 p.Gly192Arg missense_variant 0.27
thyA 3073868 p.Thr202Ala missense_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 0.95
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.93
fprA 3474400 p.Tyr132Asp missense_variant 0.3
Rv3236c 3612361 c.756C>T synonymous_variant 0.38
clpC1 4038287 c.2418C>T synonymous_variant 0.86
clpC1 4039363 p.Ala448Pro missense_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.33
embC 4239763 c.-100C>T upstream_gene_variant 0.22
embC 4239842 c.-21C>A upstream_gene_variant 0.3
embC 4241353 p.Ile497Met missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.2
ethA 4328294 c.-821C>T upstream_gene_variant 0.15
whiB6 4338377 p.Ala49Thr missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.88