TB-Profiler result

Run: ERR11082134
Summary

Run ID: ERR11082134

Sample name:

Date: 10-04-2023 02:04:19

Number of reads: 4830364

Percentage reads mapped: 99.53

Strain: lineage4.2.1.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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
gyrA 7570 p.Ala90Val missense_variant 0.64 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Tyr missense_variant 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 576108 p.Ala254Gly missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406600 c.740dupT frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475029 n.1372T>C non_coding_transcript_exon_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169041 c.1572G>A synonymous_variant 0.27
PPE35 2169044 c.1569G>C synonymous_variant 0.5
PPE35 2169047 p.Ile522Val missense_variant 0.48
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.47
PPE35 2169059 c.1554G>A synonymous_variant 0.53
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Ile missense_variant 0.53
PPE35 2169068 c.1545G>T synonymous_variant 0.52
PPE35 2169071 c.1542A>G synonymous_variant 0.39
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.19
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.62
fbiD 3339746 p.Ala210Gly missense_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0