TB-Profiler result

Run: ERR4822594
Summary

Run ID: ERR4822594

Sample name:

Date: 20-10-2023 00:57:23

Number of reads: 3974082

Percentage reads mapped: 99.61

Strain: lineage4.8;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
Rifampicin R rpoB p.Ser450Leu (0.68), rpoC p.Ile491Thr (0.46)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.99)
Pyrazinamide R pncA p.Leu182Ser (0.42), pncA p.Leu4Trp (0.23)
Streptomycin R rpsL p.Lys43Arg (0.66), rrs n.514A>C (0.36)
Fluoroquinolones R gyrA p.Ala90Val (0.53), gyrA p.Ser91Pro (0.11), gyrA p.Asp94Asn (0.36)
Moxifloxacin R gyrA p.Ala90Val (0.53), gyrA p.Ser91Pro (0.11), gyrA p.Asp94Asn (0.36)
Ofloxacin R gyrA p.Ala90Val (0.53), gyrA p.Ser91Pro (0.11), gyrA p.Asp94Asn (0.36)
Levofloxacin R gyrA p.Ala90Val (0.53), gyrA p.Ser91Pro (0.11), gyrA p.Asp94Asn (0.36)
Ciprofloxacin R gyrA p.Ala90Val (0.53), gyrA p.Ser91Pro (0.11), gyrA p.Asp94Asn (0.36)
Aminoglycosides R rrs n.1401A>G (0.37)
Amikacin R rrs n.1401A>G (0.37)
Capreomycin R rrs n.1401A>G (0.37)
Kanamycin R rrs n.1401A>G (0.37), eis c.-8C>A (0.50)
Cycloserine
Ethionamide R ethA c.1047delT (0.37), ethA c.1047delT (0.37)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.65
lineage4 Euro-American LAM;T;S;X;H None 0.37
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.64
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.38
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.64
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 0.53 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Asn missense_variant 0.36 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.46 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.66 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.36 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.37 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288697 p.Leu182Ser missense_variant 0.42 pyrazinamide
pncA 2289231 p.Leu4Trp missense_variant 0.23 pyrazinamide
eis 2715340 c.-8C>A upstream_gene_variant 0.5 kanamycin
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
ethA 4326426 c.1047delT frameshift_variant 0.37 ethionamide, 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 0.68
gyrA 9304 p.Gly668Asp missense_variant 0.62
fgd1 491742 c.960T>C synonymous_variant 0.68
mshA 575907 p.Ala187Val missense_variant 0.61
ccsA 620472 c.582C>T synonymous_variant 0.34
ccsA 620625 p.Ile245Met missense_variant 0.63
rpoB 761467 p.Leu554Pro missense_variant 0.26
rpoC 763031 c.-339T>C upstream_gene_variant 0.49
rpoC 766645 p.Glu1092Asp missense_variant 0.69
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.64
mmpL5 776182 p.Asp767Asn missense_variant 0.65
mmpS5 779615 c.-710C>G upstream_gene_variant 0.59
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.63
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.3
rpsA 1834177 c.636A>C synonymous_variant 0.63
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.74
PPE35 2167926 p.Leu896Ser missense_variant 0.59
PPE35 2167947 p.Asn889Ser missense_variant 0.38
PPE35 2167952 p.Tyr887* stop_gained 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065156 c.1035_1036insC frameshift_variant 0.42
Rv2752c 3065453 p.Gln247* stop_gained 0.41
thyA 3073715 p.Pro253Ala missense_variant 0.62
ald 3086788 c.-32T>C upstream_gene_variant 0.57
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.6
whiB7 3568759 c.-80A>C upstream_gene_variant 0.39
Rv3236c 3612813 p.Thr102Ala missense_variant 0.66
alr 3840764 c.657G>C synonymous_variant 0.33
embC 4242497 p.Arg879Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.63
aftB 4267647 p.Asp397Gly missense_variant 0.61
ethA 4326533 p.Thr314Ile missense_variant 0.65
whiB6 4338473 p.Arg17Gly missense_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.67
gid 4407927 p.Glu92Asp missense_variant 0.67
gid 4408003 p.Asp67Gly missense_variant 0.36