TB-Profiler result

Run: ERR4818792
Summary

Run ID: ERR4818792

Sample name:

Date: 01-04-2023 15:45:09

Number of reads: 253262

Percentage reads mapped: 99.62

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 1.0
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
ethA 4327386 c.87delC frameshift_variant 0.33 ethionamide, ethionamide
gid 4408115 c.87delC frameshift_variant 1.0 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 490688 c.-95G>T upstream_gene_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620340 c.450C>T synonymous_variant 0.2
ccsA 620748 c.858T>G synonymous_variant 0.25
rpoB 762194 c.2388G>A synonymous_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.75
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777020 c.1461G>A synonymous_variant 0.22
mmpL5 777891 p.Gln197Arg missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833522 c.-20G>A upstream_gene_variant 0.14
rpsA 1834378 c.837T>C synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2222450 p.Ala239Thr missense_variant 0.29
Rv1979c 2222645 p.Leu174Ile missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518383 p.Leu90Pro missense_variant 0.67
eis 2714700 c.633C>T synonymous_variant 0.29
ahpC 2725973 c.-220A>G upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339690 c.573C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640383 c.-160A>G upstream_gene_variant 0.25
fbiA 3640431 c.-112T>A upstream_gene_variant 0.25
clpC1 4039303 p.Trp468Arg missense_variant 0.4
clpC1 4039572 p.Ala378Val missense_variant 0.4
clpC1 4040182 p.Gly175Cys missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246555 c.42G>T synonymous_variant 0.18
embB 4247230 c.717G>A synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407594 c.609G>A synonymous_variant 0.18