TB-Profiler result

Run: ERR5897084
Summary

Run ID: ERR5897084

Sample name:

Date: 02-04-2023 00:47:53

Number of reads: 13804461

Percentage reads mapped: 99.5

Strain: lineage4.9;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 0.4
lineage4 Euro-American LAM;T;S;X;H None 0.6
lineage4.9 Euro-American (H37Rv-like) T1 None 0.6
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 0.65 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.33 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.62 streptomycin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.13 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.62 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.26 isoniazid, ethionamide
inhA 1674048 c.-154G>A upstream_gene_variant 0.65 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288883 p.Leu120Arg missense_variant 0.31 pyrazinamide
pncA 2289081 p.Pro54Leu missense_variant 0.59 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.94 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 0.34
gyrA 9304 p.Gly668Asp missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 0.39
mshA 576400 c.1053C>T synonymous_variant 0.61
rpoB 759746 c.-61C>T upstream_gene_variant 0.41
rpoB 759786 c.-21G>C upstream_gene_variant 0.11
rpoB 761461 p.Arg552Leu missense_variant 0.65
rpoC 762434 c.-936T>G upstream_gene_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 0.43
rpoC 764817 p.Val483Gly missense_variant 0.28
rpoC 766582 c.3213C>A synonymous_variant 0.28
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918272 c.333C>T synonymous_variant 0.3
katG 2154724 p.Arg463Leu missense_variant 0.36
PPE35 2167926 p.Leu896Ser missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.41
pncA 2289365 c.-125delC upstream_gene_variant 0.4
ahpC 2726105 c.-88G>A upstream_gene_variant 0.43
ald 3086788 c.-32T>C upstream_gene_variant 0.4
ald 3086987 p.Gln56His missense_variant 0.59
ald 3087367 p.Ala183Val missense_variant 0.55
ald 3087604 p.Ala262Glu missense_variant 0.63
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.39
alr 3841473 c.-53G>A upstream_gene_variant 0.4
rpoA 3877536 c.972C>T synonymous_variant 0.61
embC 4242075 p.Arg738Gln missense_variant 0.42
embA 4242643 c.-590C>T upstream_gene_variant 0.39
ubiA 4269124 p.Ala237Val missense_variant 0.61
whiB6 4338307 p.Ala72Gly missense_variant 0.65
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.39
gid 4407790 p.Ala138Val missense_variant 0.23