TB-Profiler result

Run: SRR3732704
Summary

Run ID: SRR3732704

Sample name:

Date: 04-04-2023 05:38:26

Number of reads: 4170259

Percentage reads mapped: 99.59

Strain: lineage4.6.2.2;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
lineage4.6 Euro-American T;LAM None 0.66
lineage4.1 Euro-American T;X;H None 0.4
lineage4.6.2 Euro-American T;LAM RD726 0.58
lineage4.1.2 Euro-American T;H None 0.42
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.58
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.47
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 7361 c.60C>T synonymous_variant 0.39
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 0.46
mshA 575679 p.Asn111Ser missense_variant 0.43
rpoB 760115 c.309C>T synonymous_variant 0.33
rpoC 765150 p.Gly594Glu missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 0.59
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168569 p.Thr682Pro missense_variant 0.44
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.33
thyX 3067474 p.Pro158Ala missense_variant 0.55
ald 3086788 c.-32T>C upstream_gene_variant 0.4
Rv3083 3448567 p.His22Asp missense_variant 0.7
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038408 p.Pro766Leu missense_variant 0.43
clpC1 4038857 c.1848C>A synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.31
aftB 4267272 p.Lys522Arg missense_variant 0.59
ethR 4326739 c.-810G>C upstream_gene_variant 0.62
ethA 4328004 c.-531C>T upstream_gene_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0