TB-Profiler result

Run: ERR4812822

Summary

Run ID: ERR4812822

Sample name:

Date: 01-04-2023 12:21:27

Number of reads: 2785513

Percentage reads mapped: 99.41

Strain: lineage4.1.2

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
lineage4.1.2 Euro-American T;H 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 490646 c.-137G>T upstream_gene_variant 0.18
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575329 c.-19C>A upstream_gene_variant 1.0
mshA 575585 p.Ala80Ser missense_variant 0.5
mshA 575652 p.Arg102Leu missense_variant 0.67
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 0.99
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766147 c.2778C>A synonymous_variant 0.22
rpoC 766204 c.2835C>A synonymous_variant 0.12
rpoC 766524 p.Arg1052Leu missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304265 c.1335C>T synonymous_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474442 n.785G>T non_coding_transcript_exon_variant 0.12
rrl 1474724 n.1067G>T non_coding_transcript_exon_variant 0.12
rrl 1474792 n.1135C>A non_coding_transcript_exon_variant 0.13
tlyA 1918191 c.252G>T synonymous_variant 1.0
katG 2155800 c.312G>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715543 c.-211G>A upstream_gene_variant 0.17
folC 2746535 p.Asn355Thr missense_variant 1.0
Rv2752c 3067040 c.-849C>A upstream_gene_variant 0.14
thyX 3067589 c.357G>T synonymous_variant 0.14
thyX 3067600 p.Val116Phe missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641361 c.-174C>T upstream_gene_variant 0.15
fbiB 3641666 c.132C>T synonymous_variant 0.11
alr 3840985 p.Arg146Cys missense_variant 0.4
clpC1 4038234 p.Arg824His missense_variant 0.29
embA 4242760 c.-473G>A upstream_gene_variant 0.17
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243829 c.597C>A synonymous_variant 0.13
embB 4245521 c.-993G>A upstream_gene_variant 0.14
embA 4245654 p.Asp808Tyr missense_variant 0.12
embA 4245752 p.Met840Ile missense_variant 0.4
embB 4245956 c.-558G>T upstream_gene_variant 0.15
embB 4246566 p.Gly18Val missense_variant 0.18
embB 4246973 p.His154Asn missense_variant 0.33
embB 4248572 p.His687Asn missense_variant 0.22
aftB 4267743 p.Arg365Leu missense_variant 0.15
aftB 4268344 p.Arg165Ser missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0