TB-Profiler result

Run: ERR5987197

Summary

Run ID: ERR5987197

Sample name:

Date: 02-04-2023 01:26:54

Number of reads: 3222492

Percentage reads mapped: 99.55

Strain: lineage2.2.2

Drug-resistance: Pre-XDR-TB


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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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_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
fgd1 490968 c.186C>T synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 0.95
mshA 575271 c.-77C>T upstream_gene_variant 0.12
mshA 575484 p.Arg46Gln missense_variant 0.15
mshA 576663 p.Ala439Val missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764020 c.651C>T synonymous_variant 0.11
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800839 p.Leu11Met missense_variant 0.15
rplC 801244 p.Arg146Ser missense_variant 0.12
fbiC 1304518 p.Ala530Thr missense_variant 0.12
fbiC 1304531 p.Ser534* stop_gained 0.12
fbiC 1304577 c.1647C>T synonymous_variant 0.11
fbiC 1305280 p.Ile784Val missense_variant 0.11
embR 1416780 p.Val190Leu missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673446 p.Ala3Ser missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155127 p.Asp329Tyr missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2222213 p.Ala318Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289319 c.-78C>T upstream_gene_variant 0.12
kasA 2518663 c.549T>C synonymous_variant 0.12
eis 2714150 p.Pro395Ser missense_variant 0.13
eis 2714162 p.Ala391Ser missense_variant 0.12
folC 2746267 c.1332C>A synonymous_variant 0.13
folC 2747080 c.519C>T synonymous_variant 0.12
pepQ 2860051 p.Arg123Leu missense_variant 0.12
ribD 2987484 p.Ala216Thr missense_variant 0.14
Rv2752c 3064596 c.1596G>A synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087761 c.942C>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613000 c.117G>T synonymous_variant 0.15
embC 4239770 c.-93C>T upstream_gene_variant 0.11
embC 4242519 p.Thr886Met missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268543 c.294C>A synonymous_variant 0.12
ubiA 4269089 p.Ala249Thr missense_variant 1.0
ubiA 4269511 c.322delG frameshift_variant 0.13
aftB 4269537 c.-701G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407916 p.Arg96His missense_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 1.0