TB-Profiler result

Run: ERR2516124
Summary

Run ID: ERR2516124

Sample name:

Date: 31-03-2023 21:19:29

Number of reads: 867233

Percentage reads mapped: 99.52

Strain: lineage4.3.2

Drug-resistance: RR-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 0.99
lineage4.3.2 Euro-American (LAM) LAM3 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
rpoB 761109 p.Asp435Asn missense_variant 0.14 rifampicin
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
ccsA 619782 c.-109C>T upstream_gene_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765500 p.Gln711Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777669 p.Ile271Asn missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303851 c.921C>A synonymous_variant 0.2
Rv1258c 1406099 c.1242C>T synonymous_variant 1.0
Rv1258c 1406537 c.804C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.99
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
inhA 1674614 p.Met138Lys missense_variant 0.13
rpsA 1834789 c.1248T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102340 p.Arg235Gly missense_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289972 c.-731T>C upstream_gene_variant 0.15
kasA 2518606 c.492G>C synonymous_variant 0.17
kasA 2518609 p.Met165Ile missense_variant 0.17
kasA 2518809 p.Lys232Arg missense_variant 0.17
folC 2746147 c.1452T>C synonymous_variant 0.2
folC 2746533 c.1065delT frameshift_variant 0.17
folC 2746537 c.1061_1062insTGCGCTC frameshift_variant 0.17
folC 2746543 c.1056C>T synonymous_variant 0.17
folC 2746546 c.1045_1052delTTCATCGA frameshift_variant 0.18
folC 2746559 p.Thr347Trp missense_variant 0.22
folC 2746561 c.1038C>G synonymous_variant 0.22
folC 2746565 c.1033_1034insTCGATGAA frameshift_variant 0.25
folC 2746569 p.Ser344Gly missense_variant 0.25
folC 2746574 c.1018_1024delGAGCGCA frameshift_variant 0.25
folC 2746584 c.1014_1015insA frameshift_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640456 c.-87G>A upstream_gene_variant 0.18
fbiA 3640772 p.Arg77Pro missense_variant 0.15
fbiA 3640774 p.Gly78Arg missense_variant 0.15
fbiB 3641733 p.Pro67Ala missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044037 p.Gly82Val missense_variant 0.14
embC 4241050 c.1188T>G synonymous_variant 0.14
embC 4241053 c.1191G>T synonymous_variant 0.15
embC 4241063 p.Ile401Leu missense_variant 0.15
embC 4241382 p.Gly507Val missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243373 p.Gln47His missense_variant 0.11
embA 4244562 p.Arg444Trp missense_variant 0.17
embA 4245428 p.Ser732Arg missense_variant 0.13
embA 4245448 p.Val739Ala missense_variant 0.15
embA 4245669 p.Ala813Thr missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
ethA 4326192 p.Glu428Gln missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407734 p.Gly157Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0