TB-Profiler result

Run: ERR4798184
Summary

Run ID: ERR4798184

Sample name:

Date: 01-04-2023 08:11:41

Number of reads: 9432067

Percentage reads mapped: 99.66

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 0.98
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 7582 p.Asp94Ala missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.95 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289207 p.Asp12Ala missense_variant 0.95 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247429 p.Met306Val missense_variant 1.0 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 0.97
gyrA 8056 p.Arg252Leu missense_variant 0.95
gyrA 9304 p.Gly668Asp missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 576108 p.Ala254Gly missense_variant 0.3
rpoB 759746 c.-61C>T upstream_gene_variant 0.97
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 764817 p.Val483Gly missense_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
katG 2156014 p.Gly33Ala missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.99
pncA 2289365 c.-125delC upstream_gene_variant 0.99
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyA 3074495 c.-24C>T 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
rpoA 3878641 c.-134C>G upstream_gene_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328212 c.-740delC upstream_gene_variant 0.97
whiB6 4338400 p.Trp41* stop_gained 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407721 p.Ala161Asp missense_variant 1.0