TB-Profiler result

Run: SRR1163036
Summary

Run ID: SRR1163036

Sample name:

Date: 02-04-2023 23:29:35

Number of reads: 7010087

Percentage reads mapped: 99.41

Strain: lineage4.1.2.1;lineage2.2.1

Drug-resistance: MDR-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
lineage2 East-Asian Beijing RD105 0.5
lineage4 Euro-American LAM;T;S;X;H None 0.49
lineage4.1 Euro-American T;X;H None 0.5
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.49
lineage4.1.2 Euro-American T;H None 0.51
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.52
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.52
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
rpoB 761109 p.Asp435Tyr missense_variant 0.54 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.5 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.46 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.92 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.63 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 0.44 pyrazinamide
pncA 2289234 c.-5_7delGACGTATGCGGG frameshift_variant&start_lost 0.46 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 0.38 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.57 ethambutol
ethA 4327033 p.Tyr147* stop_gained 0.41 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 0.5
fgd1 491742 c.960T>C synonymous_variant 0.48
mshA 575679 p.Asn111Ser missense_variant 0.56
mshA 575907 p.Ala187Val missense_variant 0.51
ccsA 620625 p.Ile245Met missense_variant 0.54
rpoB 760106 c.300G>A synonymous_variant 0.37
rpoB 760115 c.309C>T synonymous_variant 0.41
rpoB 760320 p.Gln172Lys missense_variant 0.42
rpoC 763031 c.-339T>C upstream_gene_variant 0.55
rpoC 764817 p.Val483Ala missense_variant 0.44
rpoC 765150 p.Gly594Glu missense_variant 0.45
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.5
mmpL5 776182 p.Asp767Asn missense_variant 0.47
mmpS5 779615 c.-710C>G upstream_gene_variant 0.41
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.47
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.53
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.54
PPE35 2167926 p.Leu896Ser missense_variant 0.44
PPE35 2169016 p.Thr533Ala missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.45
folC 2746747 c.852G>C synonymous_variant 0.44
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.42
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.53
embA 4243460 c.228C>T synonymous_variant 0.49
embB 4248706 c.2193G>A synonymous_variant 0.39
aftB 4267647 p.Asp397Gly missense_variant 0.51
ethA 4326864 p.Met204Val missense_variant 0.57
whiB6 4338513 c.9C>T synonymous_variant 0.49
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.51
gid 4407927 p.Glu92Asp missense_variant 0.5