TB-Profiler result

Run: ERR2514306
Summary

Run ID: ERR2514306

Sample name:

Date: 31-03-2023 20:15:28

Number of reads: 718768

Percentage reads mapped: 99.5

Strain: lineage4.1.1.3

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
tlyA 1917940 c.2delT frameshift_variant 0.15 capreomycin
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
mshA 575526 p.Pro60Gln missense_variant 0.13
rpoC 763783 c.414G>T synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766688 p.Val1107Met missense_variant 0.11
rpoC 766887 p.Thr1173Met missense_variant 0.11
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 1473587 n.-71A>G upstream_gene_variant 0.29
rrl 1476209 n.2552A>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918358 p.Thr140Ile missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519119 c.1005G>A synonymous_variant 0.13
pepQ 2860269 c.150C>T synonymous_variant 0.12
Rv2752c 3064790 p.Leu468Met missense_variant 0.12
Rv2752c 3065589 c.603C>T synonymous_variant 0.17
Rv2752c 3066008 p.Pro62Thr missense_variant 0.17
thyA 3074118 p.Leu118Phe missense_variant 0.11
thyA 3074503 c.-32G>T upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339676 p.Cys187Arg missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641845 p.Ala104Val missense_variant 0.12
rpoA 3878243 p.Glu89Gln missense_variant 1.0
embC 4242029 c.2167C>T synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245798 p.Trp856Arg missense_variant 0.12
embB 4248245 p.Ile578Val missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0