TB-Profiler result

Run: ERR5864538
Summary

Run ID: ERR5864538

Sample name:

Date: 01-04-2023 23:24:59

Number of reads: 1074897

Percentage reads mapped: 99.41

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrB 6750 p.Ala504Val missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1918696 c.759delC frameshift_variant 0.1 capreomycin, capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289222 p.Val7Ala missense_variant 0.95 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326705 c.768delG frameshift_variant 1.0 ethionamide, ethionamide
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 7707 p.Pro136Thr missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575371 c.24C>T synonymous_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620645 p.Glu252Val missense_variant 0.12
rpoB 762574 p.Gly923Asp missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763159 p.Leu1118Pro missense_variant 0.1
rpoC 764817 p.Val483Gly missense_variant 0.96
rpoC 765971 p.Ala868Thr missense_variant 0.12
rpoC 766645 p.Glu1092Asp missense_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776932 p.Asp517Tyr missense_variant 0.11
mmpR5 779254 c.267delG frameshift_variant 0.11
mmpR5 779392 p.Arg135Trp missense_variant 0.11
mmpS5 779585 c.-680A>G upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800894 p.Val29Ala missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417483 c.-136A>G upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 2155754 p.Gly120Cys missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169032 c.1581T>C synonymous_variant 0.12
PPE35 2170115 c.498G>T synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518409 p.Gly99Ser missense_variant 0.11
folC 2746511 p.Ala363Val missense_variant 0.15
ribD 2987554 p.Arg239Leu missense_variant 0.1
thyX 3067356 p.Ala197Val missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087134 p.Asp105Glu missense_variant 0.18
fbiD 3339504 p.Ile129Met missense_variant 1.0
Rv3083 3448307 c.-197T>C upstream_gene_variant 0.1
Rv3083 3448497 c.-7T>C upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568414 p.Asp89Gly missense_variant 0.17
Rv3236c 3612136 c.981C>T synonymous_variant 0.12
Rv3236c 3612220 c.897T>C synonymous_variant 0.11
Rv3236c 3612244 c.873T>C synonymous_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642776 c.1242G>C synonymous_variant 0.2
panD 4043960 c.321delT frameshift_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243702 c.473_489delGCGCCGGGACCCTGCCG frameshift_variant 0.11
embA 4244572 p.Arg447Leu missense_variant 0.11
embB 4248041 p.Ala510Thr missense_variant 0.17
embB 4248601 c.2088G>T synonymous_variant 0.12
embB 4249810 c.3297G>T stop_lost&splice_region_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338510 c.12T>C synonymous_variant 0.12
whiB6 4338563 c.-42G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0