TB-Profiler result

Run: SRR25827407
Summary

Run ID: SRR25827407

Sample name:

Date: 21-03-2024 06:39:11

Number of reads: 3316215

Percentage reads mapped: 96.17

Strain: lineage3;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 (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.23), embB p.Gly406Ala (0.77)
Pyrazinamide R pncA c.390_391dupGG (0.74), pncA c.390_391dupGG (0.74), pncA p.Leu27Pro (0.29)
Streptomycin R rpsL p.Lys43Arg (0.21), gid c.351delG (0.72)
Fluoroquinolones R gyrA p.Ala90Val (0.78), gyrA p.Asp94Asn (0.22)
Moxifloxacin R gyrA p.Ala90Val (0.78), gyrA p.Asp94Asn (0.22)
Ofloxacin R gyrA p.Ala90Val (0.78), gyrA p.Asp94Asn (0.22)
Levofloxacin R gyrA p.Ala90Val (0.78), gyrA p.Asp94Asn (0.22)
Ciprofloxacin R gyrA p.Ala90Val (0.78), gyrA p.Asp94Asn (0.22)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.73
lineage2 East-Asian Beijing RD105 0.27
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.27
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.29
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 0.78 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Asn missense_variant 0.22 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.21 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.74 pyrazinamide, pyrazinamide
pncA 2289162 p.Leu27Pro missense_variant 0.29 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.23 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.77 ethambutol
gid 4407851 c.351delG frameshift_variant 0.72 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
gyrB 5078 c.-162_-161insG upstream_gene_variant 0.3
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 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoB 759746 c.-61C>T upstream_gene_variant 0.78
rpoB 761465 c.1659G>A synonymous_variant 0.63
rpoC 762434 c.-936T>G upstream_gene_variant 0.76
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764293 c.924G>C synonymous_variant 0.56
rpoC 764817 p.Val483Gly missense_variant 0.75
rpoC 765383 p.Met672Leu missense_variant 0.14
rpoC 766488 p.Pro1040Arg missense_variant 0.28
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673772 c.-430C>A upstream_gene_variant 0.19
inhA 1673778 c.-424C>G upstream_gene_variant 0.18
inhA 1673784 c.-418G>T upstream_gene_variant 0.2
inhA 1673787 c.-415G>C upstream_gene_variant 0.21
inhA 1673799 c.-403T>C upstream_gene_variant 0.21
inhA 1673802 c.-400A>G upstream_gene_variant 0.21
inhA 1673808 c.-394A>C upstream_gene_variant 0.19
fabG1 1673829 p.Asn130Lys missense_variant 0.16
fabG1 1673830 p.Lys131Arg missense_variant 0.16
inhA 1673838 c.-364T>C upstream_gene_variant 0.17
inhA 1673841 c.-361A>G upstream_gene_variant 0.16
fabG1 1673844 p.Met135Ile missense_variant 0.17
inhA 1673847 c.-355A>C upstream_gene_variant 0.17
inhA 1673853 c.-349A>C upstream_gene_variant 0.16
inhA 1673856 c.-346T>C upstream_gene_variant 0.15
inhA 1673865 c.-337C>G upstream_gene_variant 0.18
fabG1 1673870 p.Ser144Met missense_variant 0.17
inhA 1673877 c.-325C>G upstream_gene_variant 0.17
fabG1 1673905 p.Ser156Ala missense_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.65
pncA 2289365 c.-125delC upstream_gene_variant 0.74
ahpC 2726105 c.-88G>A upstream_gene_variant 0.72
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 0.2
embC 4242075 p.Arg738Gln missense_variant 0.68
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243440 c.208C>T synonymous_variant 0.82
embA 4243460 c.228C>T synonymous_variant 0.18
embA 4245835 p.Leu868Arg missense_variant 0.17
ethA 4326676 p.Ser266Arg missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.37