TB-Profiler result

Run: ERR4800583
Summary

Run ID: ERR4800583

Sample name:

Date: 01-04-2023 09:55:38

Number of reads: 5641624

Percentage reads mapped: 99.55

Strain: lineage4.1.1.3;lineage2.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.89
lineage4 Euro-American LAM;T;S;X;H None 0.1
lineage4.1 Euro-American T;X;H None 0.11
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.9
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.89
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.11
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.1
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 0.2 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.56 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.18 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.19 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.18 ethambutol
embB 4247429 p.Met306Val missense_variant 0.85 ethambutol
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 491742 c.960T>C synonymous_variant 0.93
mshA 575907 p.Ala187Val missense_variant 0.75
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576482 p.Val379Leu missense_variant 0.19
ccsA 620553 c.663T>C synonymous_variant 0.54
ccsA 620625 p.Ile245Met missense_variant 0.86
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoC 764817 p.Val483Ala missense_variant 0.57
rpoC 765150 p.Gly594Glu missense_variant 0.12
rpoC 766488 p.Pro1040Arg missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.9
mmpL5 776182 p.Asp767Asn missense_variant 0.74
mmpS5 779615 c.-710C>G upstream_gene_variant 0.88
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.88
embR 1416569 p.Leu260Arg missense_variant 0.62
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674862 p.Gly221Ser missense_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.91
PPE35 2167926 p.Leu896Ser missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568442 p.Lys80Gln missense_variant 0.15
whiB7 3568443 p.His79Gln missense_variant 0.15
whiB7 3568854 c.-176delG upstream_gene_variant 0.19
Rv3236c 3612813 p.Thr102Ala missense_variant 0.88
rpoA 3878637 c.-130G>C upstream_gene_variant 0.22
clpC1 4040103 p.Met201Thr missense_variant 0.1
embC 4240911 p.Ala350Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.1
embA 4243460 c.228C>T synonymous_variant 0.84
embB 4246584 p.Arg24Pro missense_variant 0.36
embB 4249408 c.2895G>A synonymous_variant 0.13
embB 4249757 p.Thr1082Ala missense_variant 0.64
aftB 4267647 p.Asp397Gly missense_variant 0.82
ethA 4326513 p.Thr321Pro missense_variant 0.21
ethA 4326676 p.Ser266Arg missense_variant 0.14
ethR 4327978 p.Lys144Gln missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.89
gid 4407927 p.Glu92Asp missense_variant 0.89