TB-Profiler result

Run: ERR4832043
Summary

Run ID: ERR4832043

Sample name:

Date: 01-04-2023 21:17:19

Number of reads: 758244

Percentage reads mapped: 86.41

Strain: lineage2.2.1

Drug-resistance: MDR-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
rpoB 761095 p.Leu430Arg missense_variant 1.0 rifampicin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288766 p.Leu159Arg missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4248003 p.Gln497Pro 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
gyrB 7166 p.Ala643Thr missense_variant 0.12
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
rpoC 763031 c.-339T>C upstream_gene_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
mmpL5 776529 p.Gln651Arg missense_variant 0.16
mmpL5 779379 c.-899C>A upstream_gene_variant 0.13
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
atpE 1461289 c.245A>G splice_region_variant&stop_retained_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.2
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.18
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.22
rrs 1473101 n.1256C>A non_coding_transcript_exon_variant 0.12
rrl 1473458 n.-200G>T upstream_gene_variant 0.18
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.4
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.5
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.6
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.6
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 1.0
fabG1 1673686 p.Glu83* stop_gained 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154180 c.1932C>G synonymous_variant 0.11
katG 2154183 c.1929G>C synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155912 p.Glu67Val missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168296 p.Glu773* stop_gained 0.33
PPE35 2168684 c.1929C>A synonymous_variant 0.13
PPE35 2168867 c.1746G>T synonymous_variant 0.22
PPE35 2169117 p.Gly499Asp missense_variant 0.22
PPE35 2169865 p.Ala250Thr missense_variant 0.22
PPE35 2169992 c.621C>G synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517954 c.-161G>A upstream_gene_variant 0.12
eis 2714526 c.805_806delAC frameshift_variant 1.0
Rv2752c 3065867 c.325T>C synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4040428 p.Arg93Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly 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