TB-Profiler result

Run: ERR4797612
Summary

Run ID: ERR4797612

Sample name:

Date: 01-04-2023 07:46:42

Number of reads: 2734452

Percentage reads mapped: 99.61

Strain: lineage3

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
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
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289200 p.Cys14* stop_gained 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4407851 c.351delG frameshift_variant 1.0 streptomycin
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
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 766488 p.Pro1040Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777266 c.1215G>C synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303255 p.Thr109Ala missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472270 n.425T>A non_coding_transcript_exon_variant 0.11
rrl 1474059 n.402C>T non_coding_transcript_exon_variant 0.13
rrl 1474145 n.488T>C non_coding_transcript_exon_variant 0.12
rrl 1474260 n.603A>G non_coding_transcript_exon_variant 0.12
rrl 1474910 n.1254delG non_coding_transcript_exon_variant 0.17
rrl 1475923 n.2269delA non_coding_transcript_exon_variant 0.12
inhA 1674402 c.201C>T synonymous_variant 0.12
rpsA 1833411 c.-131G>C upstream_gene_variant 0.13
rpsA 1833446 c.-96T>C upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102019 p.Tyr342Asp missense_variant 1.0
ndh 2102932 c.111C>T synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168488 p.Ile709Phe missense_variant 0.25
PPE35 2170330 p.Ala95Thr missense_variant 0.11
PPE35 2170420 p.Met65Val missense_variant 0.1
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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067254 p.Glu231Gly missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339547 p.Leu144Ile missense_variant 0.11
fprA 3473820 c.-187C>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3640692 c.-843C>T upstream_gene_variant 0.12
rpoA 3878630 c.-123G>C upstream_gene_variant 0.15
embC 4241097 p.Ser412Leu missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244807 c.1575G>T synonymous_variant 0.1
embB 4248568 p.Trp685Cys missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0