TB-Profiler result

Run: ERR6866918
Summary

Run ID: ERR6866918

Sample name:

Date: 02-04-2023 03:41:53

Number of reads: 1964432

Percentage reads mapped: 99.47

Strain: lineage4.1.2

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
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 1472644 n.799C>T non_coding_transcript_exon_variant 0.11 streptomycin
gid 4408087 c.115delC 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
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764263 c.894G>A synonymous_variant 1.0
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
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.15
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.17
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.11
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169031 p.Asp528Asn missense_variant 0.2
PPE35 2169041 c.1572G>A synonymous_variant 0.44
PPE35 2169044 c.1569G>C synonymous_variant 0.45
PPE35 2169047 p.Ile522Val missense_variant 0.45
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.45
PPE35 2169059 c.1554G>A synonymous_variant 0.55
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Ile missense_variant 0.55
PPE35 2169068 c.1545G>T synonymous_variant 0.55
PPE35 2169071 c.1542A>G synonymous_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519143 c.1029G>A synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244293 p.Leu354Pro missense_variant 1.0
embB 4248705 p.Pro731Leu missense_variant 1.0
aftB 4267547 c.1290C>T synonymous_variant 1.0
aftB 4268333 c.504C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0