TB-Profiler result

Run: SRR17163490
Summary

Run ID: SRR17163490

Sample name:

Date: 03-04-2023 17:55:27

Number of reads: 667681

Percentage reads mapped: 99.68

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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 764817 p.Val483Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779089 c.102delG frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406962 p.Met127Val missense_variant 0.12
embR 1417184 p.Leu55Pro missense_variant 0.18
atpE 1461127 p.Asp28Gly missense_variant 0.1
atpE 1461262 p.Leu73Gln missense_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473627 n.-31T>C upstream_gene_variant 0.2
rrl 1475613 n.1956A>G non_coding_transcript_exon_variant 0.5
rrl 1476103 n.2446C>A non_coding_transcript_exon_variant 0.5
rpsA 1834884 p.Gln448Arg missense_variant 0.11
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 2168636 c.1977G>C synonymous_variant 0.11
PPE35 2170035 p.Val193Ala missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.24
PPE35 2170461 p.Gly51Glu missense_variant 1.0
PPE35 2170555 p.Gly20Arg missense_variant 0.1
Rv1979c 2222835 c.330T>A synonymous_variant 0.12
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
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242039 p.Ala726Gly missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243197 c.-35delA upstream_gene_variant 1.0
embB 4246869 p.Ser119Asn missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0