TB-Profiler result

Run: SRR6982447
Summary

Run ID: SRR6982447

Sample name:

Date: 04-04-2023 18:37:42

Number of reads: 408285

Percentage reads mapped: 99.59

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 6246 p.Lys336Arg missense_variant 0.11
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575417 p.Ala24Thr missense_variant 0.11
mshA 575607 p.Glu87Gly missense_variant 0.15
mshA 575905 c.558G>T synonymous_variant 0.12
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoC 762866 c.-504C>T upstream_gene_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766539 p.Asp1057Gly missense_variant 0.12
rpoC 767308 c.3939C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801071 p.Asp88Val missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102635 c.408C>A synonymous_variant 0.12
ndh 2102672 p.Ser124Tyr missense_variant 0.13
ndh 2102909 p.Arg45His missense_variant 0.15
PPE35 2168393 c.2220C>T synonymous_variant 0.12
PPE35 2169398 c.1214delG frameshift_variant 0.1
PPE35 2169872 c.741C>T synonymous_variant 0.11
PPE35 2169901 p.Gly238Trp missense_variant 0.1
PPE35 2170447 p.Ser56Pro missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747314 c.285A>G synonymous_variant 0.12
pepQ 2860545 c.-127G>T upstream_gene_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448626 c.123G>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568622 p.Cys20Arg missense_variant 0.17
ddn 3987288 p.Cys149Arg missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240871 p.Val337Ile missense_variant 0.18
embC 4241534 p.Pro558Thr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243102 c.-131G>T upstream_gene_variant 0.18
embB 4246699 c.186G>C synonymous_variant 0.18
embB 4247190 p.Ile226Ser missense_variant 0.12
embB 4247206 c.693C>T synonymous_variant 0.11
embB 4248206 p.Ser565Gly missense_variant 0.14
embB 4248288 p.Trp592Leu missense_variant 0.11
aftB 4268505 p.Arg111Leu missense_variant 0.15
ethA 4326013 c.1461G>T synonymous_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0