TB-Profiler result

Run: SRR1173518
Summary

Run ID: SRR1173518

Sample name:

Date: 03-04-2023 03:26:28

Number of reads: 4118309

Percentage reads mapped: 99.49

Strain: lineage4.3.3;lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.48
lineage4 Euro-American LAM;T;S;X;H None 0.51
lineage4.3 Euro-American (LAM) mainly-LAM None 0.53
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.47
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.49
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.48
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 0.49 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Gly missense_variant 0.57 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.55 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.53 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.54 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 0.59 pyrazinamide, pyrazinamide
pncA 2289038 p.Trp68Cys missense_variant 0.41 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.56 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 0.48 ethionamide
gid 4408095 c.107delT frameshift_variant 0.52 streptomycin
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 0.6
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.44
rpoB 759746 c.-61C>T upstream_gene_variant 0.56
rpoC 762434 c.-936T>G upstream_gene_variant 0.49
rpoC 763031 c.-339T>C upstream_gene_variant 0.39
rpoB 763123 p.Ile1106Thr missense_variant 0.61
rpoC 764995 c.1626C>G synonymous_variant 0.59
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.6
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.59
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.55
PPE35 2167926 p.Leu896Ser missense_variant 0.35
PPE35 2170461 p.Gly51Glu missense_variant 0.35
Rv1979c 2223051 p.Glu38Asp missense_variant 0.52
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.42
pncA 2289365 c.-125delC upstream_gene_variant 0.41
kasA 2518919 p.Gly269Ser missense_variant 0.57
ahpC 2726105 c.-88G>A upstream_gene_variant 0.45
Rv2752c 3065824 p.Pro123Leu missense_variant 0.41
thyA 3073868 p.Thr202Ala missense_variant 0.53
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.57
embC 4240172 p.Val104Met missense_variant 0.47
embC 4241562 p.Arg567His missense_variant 0.5
embC 4242075 p.Arg738Gln missense_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269271 p.Val188Ala missense_variant 0.48
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.46
gid 4408156 p.Leu16Arg missense_variant 0.66