TB-Profiler result

Run: ERR553164
Summary

Run ID: ERR553164

Sample name:

Date: 02-08-2023 09:00:39

Number of reads: NA

Percentage reads mapped: NA

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 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
ethA 4326729 c.737_744dupAGGCGGCC frameshift_variant 1.0 ethionamide, 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
gyrB 6258 p.Asp340Gly missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9484 c.2184delA frameshift_variant 0.12
gyrA 9785 c.2484G>A synonymous_variant 0.12
fgd1 490751 c.-32T>G upstream_gene_variant 0.27
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575365 c.18C>T synonymous_variant 0.13
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575982 p.Arg212Gln missense_variant 0.12
rpoB 760106 c.300G>A synonymous_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765832 c.2463G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776772 c.1708delC frameshift_variant 0.15
mmpL5 778096 p.Phe129Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417504 c.-157G>A upstream_gene_variant 0.11
embR 1417516 c.-169T>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
fabG1 1674076 p.Thr213Pro missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155653 p.Lys153Asn missense_variant 0.11
PPE35 2168563 p.Pro684Ser missense_variant 0.11
PPE35 2169712 p.Leu301Met missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289229 p.Ile5Val missense_variant 0.12
pncA 2289728 c.-487A>G upstream_gene_variant 0.18
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.29
Rv2752c 3065916 p.Phe92Leu missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448558 p.Thr19Ala missense_variant 0.2
Rv3083 3449153 p.Ile217Thr missense_variant 0.22
Rv3083 3449460 c.957T>C synonymous_variant 0.13
Rv3083 3449506 c.1006delG frameshift_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474202 p.Gln66* stop_gained 0.13
rpoA 3878259 c.249G>C synonymous_variant 0.33
clpC1 4038619 p.Lys696Glu missense_variant 0.1
clpC1 4038910 c.1794delG frameshift_variant 0.14
clpC1 4040388 p.Glu106Gly missense_variant 0.11
panD 4044132 c.150C>T synonymous_variant 0.25
embC 4241883 p.Leu674Arg missense_variant 0.13
embC 4241915 p.Gly685Cys missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243380 p.Thr50Pro missense_variant 0.18
embA 4243650 p.His140Asn missense_variant 0.13
embA 4243723 c.492_499delGGAGAAGA frameshift_variant 0.12
embA 4243733 c.501G>A synonymous_variant 0.11
embA 4243736 c.504A>T synonymous_variant 0.11
embA 4243737 p.Gln169Val missense_variant 0.11
embA 4243741 p.Val170Ala missense_variant 0.12
embA 4243742 c.510_511insTCTTCTCC frameshift_variant 0.12
embB 4248504 p.Asp664Gly missense_variant 0.11
aftB 4267573 p.His422Tyr missense_variant 0.11
aftB 4268984 c.-148T>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0