TB-Profiler result

Run: SRR16088544
Summary

Run ID: SRR16088544

Sample name:

Date: 12-01-2024 01:51:01

Number of reads: 4940299

Percentage reads mapped: 99.6

Strain: lineage4.2.1;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.Ser450Phe (0.84)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA c.-11A>G (0.74)
Streptomycin R rpsL p.Lys43Arg (0.73), rpsL p.Lys88Met (0.18)
Fluoroquinolones R gyrA p.Asp94Gly (0.76)
Moxifloxacin R gyrA p.Asp94Gly (0.76)
Ofloxacin R gyrA p.Asp94Gly (0.76)
Levofloxacin R gyrA p.Asp94Gly (0.76)
Ciprofloxacin R gyrA p.Asp94Gly (0.76)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-37G>T (0.78)
Cycloserine
Ethionamide R ethA c.1109delA (0.78)
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 0.76
lineage4 Euro-American LAM;T;S;X;H None 0.25
lineage4.2 Euro-American H;T;LAM None 0.26
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.76
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.76
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.24
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 7582 p.Asp94Gly missense_variant 0.76 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Phe missense_variant 0.84 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.73 streptomycin
rpsL 781822 p.Lys88Met missense_variant 0.18 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.74 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 0.78 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326364 c.1109delA frameshift_variant 0.78 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 491247 c.465C>T synonymous_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 0.79
mshA 575907 p.Ala187Val missense_variant 0.78
ccsA 619969 p.Val27Ile missense_variant 0.21
ccsA 620625 p.Ile245Met missense_variant 0.72
rpoC 763031 c.-339T>C upstream_gene_variant 0.78
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.76
mmpL5 776182 p.Asp767Asn missense_variant 0.72
mmpS5 779615 c.-710C>G upstream_gene_variant 0.77
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.76
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101953 p.Tyr364Asp missense_variant 0.19
katG 2154724 p.Arg463Leu missense_variant 0.76
PPE35 2167926 p.Leu896Ser missense_variant 0.77
PPE35 2169879 p.Phe245Cys missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 0.78
ald 3086742 c.-78A>C upstream_gene_variant 0.24
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.77
embA 4243460 c.228C>T synonymous_variant 0.77
embB 4249594 c.3081G>A synonymous_variant 0.28
aftB 4267647 p.Asp397Gly missense_variant 0.82
ethA 4328376 c.-903G>C upstream_gene_variant 0.28
whiB6 4338371 p.Thr51Pro missense_variant 0.74
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407927 p.Glu92Asp missense_variant 0.78