TB-Profiler result

Run: ERR4025116
Summary

Run ID: ERR4025116

Sample name:

Date: 01-04-2023 04:19:07

Number of reads: 1567474

Percentage reads mapped: 99.58

Strain: lineage4.1.1.3;lineage2.2.1

Drug-resistance: Sensitive

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 0.31
lineage4 Euro-American LAM;T;S;X;H None 0.72
lineage4.1 Euro-American T;X;H None 0.76
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.28
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.27
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.74
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.72
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
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 0.4
mshA 575907 p.Ala187Val missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 0.38
rpoC 765150 p.Gly594Glu missense_variant 0.78
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.17
mmpL5 776182 p.Asp767Asn missense_variant 0.31
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23
mmpS5 779630 c.-725T>C upstream_gene_variant 0.26
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.25
embR 1417440 c.-93G>A upstream_gene_variant 0.76
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.31
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449830 p.Tyr443His missense_variant 0.59
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.67
embA 4243460 c.228C>T synonymous_variant 0.16
embA 4243697 p.Ile155Met missense_variant 0.75
embB 4249408 c.2895G>A synonymous_variant 0.64
aftB 4267647 p.Asp397Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 0.37