TB-Profiler result

Run: SRR14782801
Summary

Run ID: SRR14782801

Sample name:

Date: 03-04-2023 11:39:49

Number of reads: 5769901

Percentage reads mapped: 99.6

Strain: lineage4.9;lineage4.1.2.1

Drug-resistance: Sensitive

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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 0.22
lineage4.9 Euro-American (H37Rv-like) T1 None 0.8
lineage4.1.2 Euro-American T;H None 0.19
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.19
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
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 0.18
gyrA 9304 p.Gly668Asp missense_variant 0.19
fgd1 491591 p.Lys270Met missense_variant 0.17
mshA 575679 p.Asn111Ser missense_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.19
mshA 576616 c.1269G>C synonymous_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 0.2
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168486 c.2127C>A synonymous_variant 0.85
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289741 c.-500T>G upstream_gene_variant 0.16
kasA 2518076 c.-39C>T upstream_gene_variant 0.12
eis 2715328 p.Thr2Ser missense_variant 0.11
pepQ 2860159 p.Ala87Gly missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 0.18
fbiD 3339734 p.Ala206Gly missense_variant 0.38
fbiD 3339746 p.Ala210Gly missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.15
fprA 3474213 p.Lys69Asn missense_variant 0.17
rpoA 3878601 c.-94C>G upstream_gene_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.64
embC 4240409 p.Pro183Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 0.19
embC 4242803 p.Val981Leu missense_variant 0.16
embB 4246529 p.Ser6Arg missense_variant 0.23
ethR 4327966 p.Thr140Ala missense_variant 0.24
whiB6 4338286 c.235delG frameshift_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0