TB-Profiler result

Run: SRR6896207
Summary

Run ID: SRR6896207

Sample name:

Date: 04-04-2023 17:58:44

Number of reads: 365050

Percentage reads mapped: 99.35

Strain: lineage4.1.2.1

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
lineage4.1.2 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
gyrA 7570 p.Ala90Val missense_variant 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
embB 4247959 p.Met482Ile missense_variant 0.11 ethambutol
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 5879 p.Thr214Ala missense_variant 0.14
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 491414 p.Val211Ala missense_variant 0.11
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
rpoB 760757 p.His317Gln missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776340 p.His714Arg missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800679 c.-130T>C upstream_gene_variant 0.12
embR 1417226 c.121delA frameshift_variant 0.11
atpE 1461109 p.Ile22Thr missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475667 n.2013delT non_coding_transcript_exon_variant 0.14
inhA 1674808 c.608delT frameshift_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102592 c.449_450delGC frameshift_variant 0.12
katG 2154222 c.1890C>T synonymous_variant 0.1
katG 2155459 p.Asn218Ser missense_variant 0.12
PPE35 2170758 c.-146A>G upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289558 c.-317C>T upstream_gene_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2859368 p.Met351Val missense_variant 0.11
thyA 3074341 p.Leu44Pro missense_variant 0.1
thyA 3074670 c.-199T>A upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087578 c.759A>G synonymous_variant 0.13
ald 3087849 p.Ser344Pro missense_variant 0.17
Rv3083 3449067 c.564G>T synonymous_variant 0.1
Rv3083 3449291 p.Lys263Met missense_variant 1.0
Rv3083 3449373 c.870C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474773 p.Ala256Glu missense_variant 0.11
fprA 3474818 p.Phe271Ser missense_variant 0.11
fprA 3475346 p.Leu447Pro missense_variant 0.14
alr 3841417 p.Lys2Glu missense_variant 0.11
ddn 3986742 c.-102G>A upstream_gene_variant 0.11
panD 4044353 c.-72A>G upstream_gene_variant 0.12
embC 4240331 p.Phe157Ile missense_variant 0.1
embC 4241823 p.Phe654Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242885 p.Lys1008Arg missense_variant 0.11
embB 4248565 c.2052C>T synonymous_variant 0.14
embB 4249317 p.Ala935Val missense_variant 0.14
aftB 4267778 c.1059T>C synonymous_variant 0.22
ubiA 4269946 c.-113G>A upstream_gene_variant 0.18
whiB6 4338571 c.-50G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338618 c.-97A>G upstream_gene_variant 0.12
gid 4407984 c.219G>C synonymous_variant 0.14
gid 4408423 c.-221G>T upstream_gene_variant 0.11