TB-Profiler result

Run: ERR4423689
Summary

Run ID: ERR4423689

Sample name:

Date: 01-04-2023 05:57:57

Number of reads: 557969

Percentage reads mapped: 99.61

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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
gid 4407851 c.351delG frameshift_variant 1.0 streptomycin
pncA 2284492 c.-448_*4188del 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 7544 p.Met81Ile missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491405 p.Met208Thr missense_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761068 p.Ile421Thr missense_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767123 p.Val1252Met missense_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674093 c.-109C>T upstream_gene_variant 0.25
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 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.53
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860518 c.-100C>A upstream_gene_variant 0.2
thyA 3073758 c.714C>A synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087186 p.Ala123Thr missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640748 p.Leu69Gln missense_variant 0.14
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240350 p.Arg163Leu missense_variant 0.17
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 1.0
embB 4246555 c.42G>C synonymous_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 1.0
ubiA 4269311 p.Trp175Gly missense_variant 1.0
whiB6 4338594 c.-73T>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0