TB-Profiler result

Run: ERR5866418
Summary

Run ID: ERR5866418

Sample name:

Date: 02-04-2023 00:40:40

Number of reads: 1302944

Percentage reads mapped: 98.2

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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155011 c.1100delC frameshift_variant 0.12 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Glu missense_variant 1.0 pyrazinamide
embB 4247399 p.Asn296His missense_variant 1.0 ethambutol
ethA 4327363 c.110delA 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620653 c.767delG frameshift_variant 0.11
rpoB 762226 p.Glu807Gly missense_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764573 p.Leu402Phe missense_variant 1.0
rpoC 765678 p.Arg770His missense_variant 1.0
rpoC 766730 p.Val1121Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304065 c.1136delC frameshift_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472480 n.635G>T non_coding_transcript_exon_variant 0.13
rrl 1473562 n.-96G>A upstream_gene_variant 0.14
rrl 1474711 n.1057_1058dupGT non_coding_transcript_exon_variant 0.17
rrl 1474890 n.1234delT non_coding_transcript_exon_variant 0.25
rrl 1475957 n.2304delC non_coding_transcript_exon_variant 0.5
rrl 1476050 n.2393G>T non_coding_transcript_exon_variant 0.33
fabG1 1673597 c.162delG frameshift_variant 0.12
fabG1 1673657 p.Thr73Lys missense_variant 0.13
inhA 1674439 p.Glu80Lys missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834983 c.1444delT frameshift_variant&stop_lost&splice_region_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103070 c.-28G>A upstream_gene_variant 0.1
katG 2154244 p.Glu623Gly missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155071 c.1041T>C synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168387 p.Gln742His missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289887 c.-646A>C upstream_gene_variant 0.17
kasA 2518441 c.327C>A synonymous_variant 0.12
kasA 2518614 p.Pro167Gln missense_variant 0.12
pepQ 2860304 p.Ser39Thr missense_variant 0.11
Rv2752c 3065760 c.431delT frameshift_variant 0.14
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339559 p.Thr148Ala missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267889 c.948C>T synonymous_variant 0.14
whiB6 4338371 p.Thr51Pro missense_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