TB-Profiler result

Run: SRR2101512
Summary

Run ID: SRR2101512

Sample name:

Date: 03-04-2023 23:45:45

Number of reads: 642752

Percentage reads mapped: 99.45

Strain: lineage4.3.2.1

Drug-resistance: Other

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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 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
folC 2747454 p.Arg49Trp missense_variant 0.14 para-aminosalicylic_acid
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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761223 p.His473Thr missense_variant 0.15
rpoB 762673 p.Glu956Val missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765201 p.Val611Asp missense_variant 0.15
rpoC 766839 p.Ile1157Thr missense_variant 0.12
rpoC 767215 c.3846G>A synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776423 p.Asp686Glu missense_variant 0.11
mmpL5 777626 p.Tyr285* stop_gained 0.12
mmpL5 777864 c.616delG frameshift_variant 0.17
mmpL5 777879 p.Asp201Gly missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303975 p.Ala349Thr missense_variant 0.17
Rv1258c 1406630 c.711G>A synonymous_variant 0.11
Rv1258c 1406711 c.630C>A synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
inhA 1674036 c.-166G>A upstream_gene_variant 0.11
fabG1 1674113 p.Ala225Asp missense_variant 0.29
fabG1 1674168 p.Met243Ile missense_variant 0.17
inhA 1674443 p.Ala81Glu missense_variant 0.13
inhA 1674603 c.402G>T synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918660 p.Leu241Met missense_variant 0.17
katG 2155008 c.1104C>T synonymous_variant 0.13
katG 2155408 p.Pro235Leu missense_variant 0.15
katG 2156166 c.-55T>C upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518371 c.260delG frameshift_variant 0.13
kasA 2518634 p.Gly174Ser missense_variant 0.92
eis 2715509 c.-177G>T upstream_gene_variant 0.15
folC 2746208 p.Thr464Asn missense_variant 0.15
folC 2747248 c.351G>A synonymous_variant 0.13
folC 2747528 p.Ile24Asn missense_variant 0.12
pepQ 2859449 p.Val324Met missense_variant 0.13
pepQ 2860472 c.-54G>C upstream_gene_variant 0.12
ribD 2987599 p.Arg254His missense_variant 0.18
thyX 3067521 p.Thr142Asn missense_variant 0.12
thyX 3068120 c.-175C>G upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339069 c.-49C>A upstream_gene_variant 0.14
fbiD 3339086 c.-32G>T upstream_gene_variant 0.12
fbiD 3339266 p.Ala50Glu missense_variant 0.25
fbiD 3339413 p.Ala99Asp missense_variant 0.25
fbiD 3339617 p.Ser167Tyr missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475001 p.Leu332Arg missense_variant 0.12
fbiA 3641525 p.Gly328Val missense_variant 0.12
clpC1 4038257 c.2448G>A synonymous_variant 0.15
clpC1 4038274 p.Gly811Cys missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040868 c.-164T>C upstream_gene_variant 0.15
embC 4240444 c.582C>A synonymous_variant 0.12
embC 4241019 p.Leu386Pro missense_variant 0.12
embC 4241532 p.Ile557Thr missense_variant 0.13
embC 4241780 p.Trp640Arg missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243358 c.126C>A synonymous_variant 0.14
embA 4243516 p.Ala95Val missense_variant 0.2
embA 4244209 p.Leu326Gln missense_variant 0.2
embA 4244447 c.1215G>C synonymous_variant 0.14
embA 4244710 p.Ile493Asn missense_variant 0.17
embB 4246938 p.Ser142Tyr missense_variant 0.12
embB 4248839 p.Pro776Ala missense_variant 0.22
embB 4249000 c.2487T>G synonymous_variant 0.17
aftB 4268190 c.646delG frameshift_variant 0.12
aftB 4268883 c.-47G>T upstream_gene_variant 0.2
ubiA 4268935 p.Ala300Asp missense_variant 0.13
ubiA 4268972 c.859_861delCTG conservative_inframe_deletion 0.12
ubiA 4268996 p.Arg280Gly missense_variant 0.13
aftB 4269042 c.-206G>A upstream_gene_variant 0.2
ubiA 4270020 c.-187C>T upstream_gene_variant 0.17
ethR 4327654 c.108delT frameshift_variant 0.12
whiB6 4338341 p.Leu61Met missense_variant 0.15
whiB6 4338352 p.Pro57Gln missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0