TB-Profiler result

Run: ERR028614
Summary

Run ID: ERR028614

Sample name:

Date: 31-03-2023 08:24:25

Number of reads: 1086617

Percentage reads mapped: 99.5

Strain: lineage4.1.2.1

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
lineage4.1 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 0.99
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
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 0.91
fgd1 491014 p.Thr78Pro missense_variant 0.38
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762249 p.Leu815Val missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474007 n.350A>C non_coding_transcript_exon_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.25
rpsA 1833958 p.Ile139Met missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.25
PPE35 2169866 c.747G>C synonymous_variant 0.47
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.5
pepQ 2859381 c.1038C>G synonymous_variant 0.6
ribD 2987396 c.558T>G synonymous_variant 0.22
thyA 3073806 c.666C>G synonymous_variant 0.54
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.25
clpC1 4039932 p.Gly258Val missense_variant 0.37
embC 4239842 c.-21C>A upstream_gene_variant 0.2
embC 4239973 c.111T>G synonymous_variant 0.2
embC 4242425 p.Arg855Gly missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.3
embA 4244905 p.Val558Gly missense_variant 0.25
embB 4246941 p.Pro143Leu missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0