TB-Profiler result

Run: SRR998818
Summary

Run ID: SRR998818

Sample name:

Date: 04-04-2023 23:37:25

Number of reads: 599714

Percentage reads mapped: 99.35

Strain: lineage4.1.2.1

Drug-resistance: HR-TB

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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 0.99
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777663 p.Ala273Val missense_variant 0.2
mmpS5 778600 p.Asn102Lys missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801253 p.Gly149Ser missense_variant 0.14
fbiC 1304802 c.1872G>C synonymous_variant 0.1
fbiC 1304904 c.1974G>A synonymous_variant 0.14
embR 1416432 p.Ala306Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476164 n.2507A>T non_coding_transcript_exon_variant 0.12
rrl 1476195 n.2538C>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154822 c.1290G>T synonymous_variant 0.18
PPE35 2167846 p.Ser923Gly missense_variant 0.11
PPE35 2169783 p.Thr277Lys missense_variant 1.0
PPE35 2170431 p.Ser61Leu missense_variant 0.22
PPE35 2170634 c.-22T>C upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289011 c.231C>A synonymous_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714253 c.1080C>T synonymous_variant 0.17
folC 2747505 p.His32Asn missense_variant 0.15
ribD 2986716 c.-123T>G upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448923 c.420C>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038988 p.Asp573Tyr missense_variant 0.11
panD 4044290 c.-9G>T upstream_gene_variant 0.14
embC 4241316 p.Ile485Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249737 p.Pro1075Arg missense_variant 0.13
aftB 4267883 p.Ser318Arg missense_variant 0.15
ethA 4328464 c.-991C>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0