TB-Profiler result

Run: ERR1213919
Summary

Run ID: ERR1213919

Sample name:

Date: 31-03-2023 12:44:16

Number of reads: 2126078

Percentage reads mapped: 97.91

Strain: lineage4.3

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 0.96
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 761155 p.Ser450Trp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrB 5990 p.Phe251Val missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620016 c.126C>T synonymous_variant 0.25
rpoC 763546 c.177A>G synonymous_variant 0.17
rpoC 763594 c.225C>T synonymous_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766184 p.Glu939Lys missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781799 c.240G>T synonymous_variant 0.18
Rv1258c 1407539 c.-199C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.67
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.25
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.33
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.4
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.29
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.4
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.4
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.4
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.25
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.33
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.33
inhA 1673718 c.-484G>A upstream_gene_variant 0.18
inhA 1673865 c.-337C>A upstream_gene_variant 0.18
inhA 1673967 c.-235G>A upstream_gene_variant 0.29
rpsA 1833544 c.3G>T start_lost 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102233 c.810G>A synonymous_variant 0.18
ndh 2102242 c.801G>A synonymous_variant 0.18
katG 2156088 c.24T>A synonymous_variant 0.18
PPE35 2169320 p.Leu431Phe missense_variant 0.21
PPE35 2169866 c.747G>C synonymous_variant 0.2
PPE35 2169994 p.Leu207Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087519 c.700_701insA frameshift_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841441 c.-21C>A upstream_gene_variant 1.0
rpoA 3877818 c.690A>G synonymous_variant 0.4
rpoA 3877839 c.669G>C synonymous_variant 0.5
rpoA 3877857 c.651G>A synonymous_variant 0.33
rpoA 3877866 c.642G>C synonymous_variant 0.4
ddn 3986943 p.Gly34Arg missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044188 c.94T>C synonymous_variant 0.2
embC 4241617 c.1756dupT frameshift_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245479 p.Met749Ile missense_variant 0.2
ethR 4328017 p.Arg157Ser missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>G upstream_gene_variant 1.0
whiB6 4338602 c.-81A>T upstream_gene_variant 1.0