TB-Profiler result

Run: ERR5987364
Summary

Run ID: ERR5987364

Sample name:

Date: 02-04-2023 01:33:33

Number of reads: 3748391

Percentage reads mapped: 99.44

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 0.99
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 761110 p.Asp435Val 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 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine
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 8981 c.1680G>C synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575435 p.Pro30Thr missense_variant 0.12
mshA 575848 c.501C>T synonymous_variant 0.11
ccsA 619966 p.Val26Met missense_variant 0.18
ccsA 620711 p.Val274Glu missense_variant 0.11
ccsA 620831 p.Thr314Ile missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766822 c.3455delA frameshift_variant 0.13
rpoC 767088 p.Cys1240Phe missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778329 p.Pro51Leu missense_variant 0.12
mmpR5 779324 p.Ala112Asp missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801283 c.478delG frameshift_variant 0.1
fbiC 1304063 p.Ala378Val missense_variant 0.12
fbiC 1305021 c.2091C>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673336 c.-103delA upstream_gene_variant 0.13
fabG1 1673504 p.Gly22Val 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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519003 c.889C>T synonymous_variant 0.15
pepQ 2859417 c.1002C>T synonymous_variant 0.15
pepQ 2860123 p.Ser99Ile missense_variant 0.12
thyX 3067656 p.Arg97Gln missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339269 p.Ala51Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612893 p.Leu75Pro missense_variant 0.1
fbiB 3641951 c.417G>T synonymous_variant 0.11
ddn 3987056 c.213G>A synonymous_variant 0.12
clpC1 4038488 c.2217C>T synonymous_variant 0.14
clpC1 4038519 p.Arg729Leu missense_variant 0.15
embA 4242271 c.-962A>G upstream_gene_variant 0.11
embA 4242505 c.-728G>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242911 p.Gly1017Ser missense_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245965 c.-549A>G upstream_gene_variant 0.13
embA 4246123 p.Leu964Gln missense_variant 0.13
aftB 4267632 c.1204delG frameshift_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268780 p.Trp19Cys missense_variant 0.12
ubiA 4270005 c.-172C>T upstream_gene_variant 0.15
whiB6 4338346 p.Arg59Gln missense_variant 0.13
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