TB-Profiler result

Run: ERR4832055
Summary

Run ID: ERR4832055

Sample name:

Date: 01-04-2023 21:17:35

Number of reads: 1318120

Percentage reads mapped: 87.39

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 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
pncA 2273378 c.-70_*15302del transcript_ablation 1.0 pyrazinamide
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
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 776658 p.Asp608Gly missense_variant 0.14
mmpL5 776748 p.Phe578Ser missense_variant 0.12
mmpL5 777013 p.Lys490Glu missense_variant 0.1
mmpS5 778803 p.Glu35* stop_gained 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
rrs 1471776 n.-70G>T upstream_gene_variant 0.11
rrs 1472556 n.711C>A non_coding_transcript_exon_variant 0.17
rrs 1472778 n.933C>A non_coding_transcript_exon_variant 0.11
rrl 1474781 n.1124C>T non_coding_transcript_exon_variant 0.29
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 0.4
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.4
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.5
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.5
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.67
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.67
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 2168258 c.2355G>T synonymous_variant 0.15
PPE35 2168419 p.Asp732Tyr missense_variant 0.12
PPE35 2168465 c.2148C>A synonymous_variant 0.12
Rv1979c 2221889 p.Val426Ile missense_variant 1.0
Rv1979c 2222172 c.993G>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.33
ahpC 2726338 p.Val49Gly missense_variant 0.22
ahpC 2726341 p.Val50Gly missense_variant 0.27
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246085 p.Glu951Asp missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268456 c.381G>A synonymous_variant 1.0
ethA 4326379 c.1095G>T synonymous_variant 0.12
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