TB-Profiler result

Run: ERR4827451
Summary

Run ID: ERR4827451

Sample name:

Date: 01-04-2023 18:04:06

Number of reads: 1090614

Percentage reads mapped: 99.32

Strain: lineage2.2.1

Drug-resistance: MDR-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
lineage2.2.1 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289072 p.His57Arg missense_variant 1.0 pyrazinamide
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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576579 p.Gly411Val missense_variant 0.15
mshA 576581 c.1236_1272delACGGGGACGGGTGATGAGCCGGGCGGCGGCACGGCAC frameshift_variant 0.22
mshA 576746 p.Gly467Ser missense_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764669 p.Pro434Thr missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775912 c.2569C>A synonymous_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 779052 c.-572T>C upstream_gene_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
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
PPE35 2170048 p.Leu189Val missense_variant 0.46
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449282 p.Arg260His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612293 p.Phe275Ser missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841403 p.Glu6Asp missense_variant 1.0
clpC1 4040144 c.561G>C synonymous_variant 0.18
clpC1 4040242 p.Thr155Ser missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245965 c.-549A>G upstream_gene_variant 0.18
embB 4246355 c.-159G>A upstream_gene_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.36
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4248631 c.2118G>A synonymous_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267894 p.Ile315Phe missense_variant 0.2
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 4407917 p.Arg96Cys missense_variant 0.15
gid 4407927 p.Glu92Asp missense_variant 1.0