TB-Profiler result

Run: ERR5866420
Summary

Run ID: ERR5866420

Sample name:

Date: 02-04-2023 00:40:42

Number of reads: 1119034

Percentage reads mapped: 98.25

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 0.9 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155011 c.1100delC frameshift_variant 0.18 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 491292 c.513delC frameshift_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619824 c.-67T>C upstream_gene_variant 0.17
ccsA 620554 c.666_667dupCC frameshift_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759711 c.-96G>A upstream_gene_variant 0.2
rpoB 760648 p.Pro281Leu missense_variant 0.17
rpoB 762226 p.Glu807Gly missense_variant 0.69
rpoB 762571 p.Ile922Thr missense_variant 0.11
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
rpoC 767081 p.Ile1238Val missense_variant 0.12
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 778851 p.Ala19Ser missense_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800954 p.Ala49Asp missense_variant 0.11
fbiC 1304007 c.1079delT frameshift_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472461 n.616G>C non_coding_transcript_exon_variant 0.11
rrs 1472462 n.617T>C non_coding_transcript_exon_variant 0.11
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.11
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.11
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.12
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.16
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.18
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.18
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.17
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.17
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.21
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.16
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.1
rrl 1476433 n.2776C>T non_coding_transcript_exon_variant 0.25
fabG1 1673861 p.Val141Asp missense_variant 0.11
inhA 1674237 c.36T>A synonymous_variant 0.12
inhA 1674653 p.Pro151Leu missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154517 p.Ala532Val missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 0.11
Rv1979c 2223043 p.Gly41Glu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859601 c.817delG frameshift_variant 0.13
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449132 p.Leu210Pro missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474785 p.Pro260His missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241688 p.Thr609Met missense_variant 0.11
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
embA 4245411 p.Ser727Gly missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
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 0.97