TB-Profiler result

Run: ERR11081543
Summary

Run ID: ERR11081543

Sample name:

Date: 09-04-2023 02:13:05

Number of reads: 2748450

Percentage reads mapped: 99.56

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 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
gid 4408100 c.102delG frameshift_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 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.2
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576113 p.Arg256Gly missense_variant 0.25
mshA 576456 p.Val370Gly missense_variant 0.17
mshA 576616 c.1269G>C synonymous_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.16
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765773 p.Ile802Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.16
fabG1 1673553 p.Asp38Glu missense_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.32
pepQ 2860159 p.Ala87Gly missense_variant 0.32
Rv2752c 3064823 p.Val457Leu missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.22
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fbiD 3339751 p.Ala212Pro missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474213 p.Lys69Asn missense_variant 0.13
rpoA 3878597 c.-90G>C upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.7
clpC1 4040087 c.618G>A synonymous_variant 0.99
embC 4240409 p.Pro183Ala missense_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.3
embB 4247016 p.Ser168Trp missense_variant 0.19
embB 4247020 c.507C>G synonymous_variant 0.37
embB 4248328 c.1815G>C synonymous_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0