TB-Profiler result

Run: ERR5897074
Summary

Run ID: ERR5897074

Sample name:

Date: 02-04-2023 00:47:34

Number of reads: 4667535

Percentage reads mapped: 99.29

Strain: lineage3

Drug-resistance: Pre-XDR-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
gyrA 7570 p.Ala90Val missense_variant 0.37 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.39 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.59 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.66 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.4 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288824 p.Arg140Gly missense_variant 0.59 pyrazinamide
pncA 2288839 p.Thr135Pro missense_variant 0.41 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.31 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.67 ethambutol
ethA 4327091 c.382dupG frameshift_variant 0.41 ethionamide, ethionamide
gid 4408100 c.102delG frameshift_variant 0.33 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 0.99
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
rpoB 762427 p.Ser874Tyr missense_variant 0.67
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.41
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777820 c.661C>T synonymous_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674135 c.-67C>T upstream_gene_variant 0.65
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101854 c.1187_1188dupGG frameshift_variant 0.26
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser 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
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
alr 3840952 p.Lys157Glu missense_variant 0.42
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243204 c.-28delT upstream_gene_variant 0.57
ethA 4326419 p.Ala352Glu missense_variant 0.61
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0