TB-Profiler result

Run: ERR9119906
Summary

Run ID: ERR9119906

Sample name:

Date: 02-04-2023 10:12:42

Number of reads: 5472119

Percentage reads mapped: 98.82

Strain: lineage4.9.1;lineage2.2.1

Drug-resistance: MDR-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 0.28
lineage4 Euro-American LAM;T;S;X;H None 0.75
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.24
lineage4.9 Euro-American (H37Rv-like) T1 None 0.75
lineage4.9.1 Euro-American (H37Rv-like) T1 None 0.75
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.24
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
rpoB 761109 p.Asp435Tyr missense_variant 0.21 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.27 isoniazid
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 0.29
gyrA 8978 c.1677C>T synonymous_variant 0.72
gyrA 9304 p.Gly668Asp missense_variant 0.31
fgd1 491742 c.960T>C synonymous_variant 0.21
mshA 575907 p.Ala187Val missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.35
rpoC 764205 p.Asp279Gly missense_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.26
mmpS5 779615 c.-710C>G upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.32
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
pncA 2289138 p.Leu35Arg missense_variant 0.7
pncA 2289723 c.-482C>A upstream_gene_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 0.22
fbiD 3339385 p.Asp90Asn missense_variant 0.76
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 0.32
embC 4240423 c.561G>A synonymous_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 0.31
embA 4243460 c.228C>T synonymous_variant 0.26
embB 4246076 c.-438G>A upstream_gene_variant 0.79
aftB 4267647 p.Asp397Gly missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.2
gid 4407927 p.Glu92Asp missense_variant 0.21