TB-Profiler result

Run: ERR4407456
Summary

Run ID: ERR4407456

Sample name:

Date: 01-04-2023 05:44:51

Number of reads: 235353

Percentage reads mapped: 78.7

Strain: lineage4.1.2.1

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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 6927 p.Leu563Trp missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.38
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778421 c.-569C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.14
rrs 1472928 n.1083A>G non_coding_transcript_exon_variant 0.18
inhA 1673724 c.-478A>G upstream_gene_variant 0.17
rpsA 1834464 p.Gly308Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155222 p.Gly297Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746668 p.Ala311Pro missense_variant 0.17
folC 2746752 p.Gly283Ser missense_variant 1.0
folC 2747715 c.-117G>C upstream_gene_variant 0.25
Rv2752c 3064707 c.1485G>T synonymous_variant 0.15
Rv2752c 3065008 p.Pro395Leu missense_variant 0.12
Rv2752c 3065431 p.Ala254Glu missense_variant 0.5
thyA 3074281 p.Arg64His missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087266 c.447G>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474782 p.Glu259Gly missense_variant 0.2
fbiB 3640851 c.-684G>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4267074 p.Leu588Pro missense_variant 0.14
ethA 4328276 c.-803C>T upstream_gene_variant 0.25
ethA 4328444 c.-971C>G upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0