TB-Profiler result

Run: SRR1163172
Summary

Run ID: SRR1163172

Sample name:

Date: 02-04-2023 23:32:51

Number of reads: 2656518

Percentage reads mapped: 99.39

Strain: lineage4.3.3;lineage2.2.1

Drug-resistance: Pre-XDR-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 0.77
lineage4 Euro-American LAM;T;S;X;H None 0.29
lineage4.3 Euro-American (LAM) mainly-LAM None 0.25
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.75
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.77
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.25
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 7563 p.Gly88Cys missense_variant 0.25 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.79 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.71 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.25 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.98 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.28 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 0.19 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289248 c.-7T>C upstream_gene_variant 0.14 pyrazinamide
eis 2715340 c.-8C>A upstream_gene_variant 0.24 kanamycin
folC 2747480 p.Glu40Gly missense_variant 0.77 para-aminosalicylic_acid
embB 4247431 p.Met306Ile missense_variant 0.77 ethambutol
embB 4247469 p.Tyr319Ser missense_variant 0.28 ethambutol
ethA 4326320 p.Gly385Asp missense_variant 0.73 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 8040 p.Gly247Ser missense_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.79
mshA 575907 p.Ala187Val missense_variant 0.71
ccsA 620625 p.Ile245Met missense_variant 0.72
rpoC 763031 c.-339T>C upstream_gene_variant 0.78
rpoC 764918 p.Val517Leu missense_variant 0.78
rpoC 764995 c.1626C>G synonymous_variant 0.35
rpoC 766487 p.Pro1040Thr missense_variant 0.35
rpoC 767007 p.Ala1213Glu missense_variant 0.77
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.68
mmpL5 776182 p.Asp767Asn missense_variant 0.72
mmpS5 779615 c.-710C>G upstream_gene_variant 0.78
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.18
fbiC 1304962 p.Trp678Gly missense_variant 0.27
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.73
rpsA 1834429 c.888C>T synonymous_variant 0.69
rpsA 1834836 p.Met432Thr missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.66
katG 2156196 c.-85C>T upstream_gene_variant 0.26
PPE35 2167926 p.Leu896Ser missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288790 p.Leu151Trp missense_variant 0.75
kasA 2518919 p.Gly269Ser missense_variant 0.26
folC 2746340 p.Ala420Val missense_variant 0.28
ribD 2986827 c.-12G>A upstream_gene_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 0.18
ald 3086731 c.-89A>G upstream_gene_variant 0.74
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 0.79
clpC1 4038287 c.2418C>T synonymous_variant 0.25
clpC1 4038968 c.1737G>A synonymous_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.78
embA 4243460 c.228C>T synonymous_variant 0.74
aftB 4267647 p.Asp397Gly missense_variant 0.83
whiB6 4338371 p.Thr51Pro missense_variant 0.74
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.69
gid 4407927 p.Glu92Asp missense_variant 0.84