TB-Profiler result

Run: ERR8975664
Summary

Run ID: ERR8975664

Sample name:

Date: 02-04-2023 08:57:14

Number of reads: 3873535

Percentage reads mapped: 99.8

Strain: lineage4.3.2.1;lineage2.2.2

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 0.17
lineage4 Euro-American LAM;T;S;X;H None 0.85
lineage4.3 Euro-American (LAM) mainly-LAM None 0.84
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.18
lineage4.3.2 Euro-American (LAM) LAM3 None 0.82
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.16
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.82
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 7572 p.Ser91Pro missense_variant 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.15 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.24 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.22 isoniazid, ethionamide
inhA 1674048 c.-154G>A upstream_gene_variant 0.82 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.13 isoniazid
pncA 2288724 c.517dupG frameshift_variant 0.16 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.18 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 0.29 ethionamide
gid 4407967 p.Leu79Ser missense_variant 0.16 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 5520 p.Pro94Leu missense_variant 0.79
gyrA 7222 c.-80C>T upstream_gene_variant 0.78
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 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 0.81
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.79
rpsA 1834177 c.636A>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.14
Rv1979c 2221939 p.Arg409Gln missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.81
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
clpC1 4038287 c.2418C>T synonymous_variant 0.81
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.13
embB 4248371 p.Arg620Cys missense_variant 0.91
aftB 4267647 p.Asp397Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 0.16
gid 4408156 p.Leu16Arg missense_variant 0.86