TB-Profiler result

Run: ERR2510164
Summary

Run ID: ERR2510164

Sample name:

Date: 31-03-2023 18:34:45

Number of reads: 4723135

Percentage reads mapped: 99.58

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 0.93
lineage4.1.2 Euro-American T;H None 0.91
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.92
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 4408087 c.115delC frameshift_variant 0.11 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 0.91
mshA 575679 p.Asn111Ser missense_variant 0.92
rpoB 760115 c.309C>T synonymous_variant 0.93
rpoB 761889 p.Val695Leu missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778554 p.Val118Ile missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 0.92
thyA 3073806 c.666C>G synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.9
fprA 3474299 p.Asp98Gly missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.91
whiB6 4338595 c.-75delG upstream_gene_variant 1.0