TB-Profiler result

Run: ERR4827957
Summary

Run ID: ERR4827957

Sample name:

Date: 01-04-2023 18:34:49

Number of reads: 4118374

Percentage reads mapped: 99.5

Strain: lineage4.5;lineage2.2.1

Drug-resistance: Other

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 0.13
lineage4.5 Euro-American H;T RD122 0.13
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.9
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.87
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
rpsL 781687 p.Lys43Arg missense_variant 0.83 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
gyrA 7362 p.Glu21Gln missense_variant 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 0.13
gyrA 8042 c.741C>T synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.87
mshA 575907 p.Ala187Val missense_variant 0.87
mshA 576108 p.Ala254Gly missense_variant 0.25
ccsA 619815 c.-76G>C upstream_gene_variant 0.86
ccsA 620625 p.Ile245Met missense_variant 0.92
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 766645 p.Glu1092Asp missense_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpL5 776182 p.Asp767Asn missense_variant 0.87
mmpL5 776371 p.Gly704Cys missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674026 c.-176A>C upstream_gene_variant 0.9
rpsA 1834177 c.636A>C synonymous_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.9
PPE35 2167926 p.Leu896Ser missense_variant 0.84
PPE35 2169144 p.Val490Ala missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.11
PPE35 2170521 p.Trp31* stop_gained 0.17
PPE35 2170568 p.Ile15Met missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.88
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.85
clpC1 4038318 p.Pro796Leu missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.92
embB 4246555 c.42G>C synonymous_variant 0.11
embB 4246556 p.Ala15Pro missense_variant 0.11
embB 4246584 p.Arg24Pro missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 0.92
ubiA 4269871 c.-38G>A upstream_gene_variant 0.88
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.91
gid 4407927 p.Glu92Asp missense_variant 0.87