TB-Profiler result

Run: ERR4831837
Summary

Run ID: ERR4831837

Sample name:

Date: 01-04-2023 21:09:22

Number of reads: 1819227

Percentage reads mapped: 86.9

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 761140 p.His445Arg missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288841 p.Ala134Val missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>G upstream_gene_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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765509 p.Asp714Asn 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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.29
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.56
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.57
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.44
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.4
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.4
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.34
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.34
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.37
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.38
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.17
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.18
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.18
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 0.2
rrl 1474586 n.929T>A non_coding_transcript_exon_variant 0.2
rrl 1474587 n.930G>A non_coding_transcript_exon_variant 0.2
rrl 1474602 n.945C>G non_coding_transcript_exon_variant 0.18
rrl 1474608 n.951T>G non_coding_transcript_exon_variant 0.18
rrl 1474609 n.952G>C non_coding_transcript_exon_variant 0.18
rrl 1474610 n.953C>T non_coding_transcript_exon_variant 0.18
rrl 1474862 n.1205C>T non_coding_transcript_exon_variant 0.15
rrl 1475008 n.1351C>T non_coding_transcript_exon_variant 0.25
rrl 1475440 n.1783T>C non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.21
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.25
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 0.96
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 2168435 c.2178C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714566 p.Leu256Pro missense_variant 0.17
ahpC 2726341 p.Val50Gly missense_variant 0.31
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
rpoA 3878543 c.-36G>C upstream_gene_variant 0.11
rpoA 3878615 c.-108C>T upstream_gene_variant 1.0
rpoA 3878633 c.-126C>A upstream_gene_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249738 c.3225C>T synonymous_variant 0.12
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