TB-Profiler result

Run: SRR2101511
Summary

Run ID: SRR2101511

Sample name:

Date: 03-04-2023 23:45:38

Number of reads: 401052

Percentage reads mapped: 99.61

Strain: lineage4.1.1.3

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
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
gyrB 5255 p.Lys6* stop_gained 0.11
gyrA 7340 c.39C>T synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8327 c.1026C>T synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491488 p.Asp236Asn missense_variant 0.12
mshA 576751 p.Lys468Asn missense_variant 0.33
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765916 p.Tyr849* stop_gained 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
fbiC 1304136 c.1206C>A synonymous_variant 0.18
Rv1258c 1407522 c.-182C>T upstream_gene_variant 0.1
embR 1417209 c.138delC frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473813 n.156C>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169554 c.1058delA frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860589 c.-171G>A upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.92
fbiB 3641325 c.-210G>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249524 p.Asn1004Ile missense_variant 0.18
aftB 4267128 p.Ala570Glu missense_variant 0.12
aftB 4268671 p.Glu56* stop_gained 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0
gid 4407978 c.225G>T synonymous_variant 0.14
gid 4408336 c.-134T>C upstream_gene_variant 1.0