TB-Profiler result

Run: ERR4797042
Summary

Run ID: ERR4797042

Sample name:

Date: 01-04-2023 07:19:12

Number of reads: 4487844

Percentage reads mapped: 99.64

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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
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 490756 c.-27T>G upstream_gene_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.16
mshA 576113 p.Arg256Gly missense_variant 0.36
mshA 576616 c.1269G>C synonymous_variant 0.38
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781676 c.117C>T synonymous_variant 1.0
Rv1258c 1406242 p.Ala367Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471793 n.-53G>T upstream_gene_variant 0.31
rrs 1471805 n.-41C>A upstream_gene_variant 0.45
rrs 1471812 n.-34C>A upstream_gene_variant 0.2
rrs 1472650 n.805A>G non_coding_transcript_exon_variant 0.33
rrl 1473400 n.-258C>T upstream_gene_variant 0.25
rrl 1474479 n.822A>G non_coding_transcript_exon_variant 1.0
rrl 1476068 n.2411C>A non_coding_transcript_exon_variant 0.25
fabG1 1674079 p.Pro214Ala missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.16
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.15
fbiD 3339044 c.-74T>G upstream_gene_variant 0.19
fbiD 3339734 p.Ala206Gly missense_variant 0.8
fbiD 3339749 p.Val211Gly missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474208 p.Glu68* stop_gained 0.23
embC 4240409 p.Pro183Ala missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243700 c.468C>A synonymous_variant 0.25
embB 4247033 p.Ser174Cys missense_variant 0.21
aftB 4268619 p.Val73Gly missense_variant 0.33
ethA 4326041 p.Leu478Arg missense_variant 1.0
whiB6 4338200 p.Asp108His missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0