TB-Profiler result

Run: ERR2228890
Summary

Run ID: ERR2228890

Sample name:

Date: 2024-04-14T07:00:20.234775

Number of reads: 153319

Percentage reads mapped: 17.42

Median coverage: 3.0

Strain: lineage4.8;lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.4
lineage4.9 Euro-American (H37Rv-like) None 0.74
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance Mutation from literature
amikacin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 1.0 capreomycin Assoc w R
kanamycin Assoc w R
amikacin Assoc w R
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 Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 762899 c.-471G>T upstream_gene_variant 0.67 rifampicin
rpoB 762920 c.3114C>T synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoC 762959 c.-411G>T upstream_gene_variant 0.75 rifampicin
rpoC 762971 c.-399G>C upstream_gene_variant 0.67 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.47 rifampicin
rpoB 762989 c.3183G>A synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 763534 c.165T>C synonymous_variant 0.7 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.71 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.83 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.83 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.79 rifampicin Not assoc w R - Interim
rpoC 763622 p.Ala85Ser missense_variant 0.89 rifampicin Uncertain significance
rpoC 763627 p.Lys86Asn missense_variant 0.88 rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.82 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.64 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.64 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.77 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.79 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.79 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.85 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.91 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.95 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.95 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.95 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833970 c.429G>C synonymous_variant 0.79 pyrazinamide
rpsA 1833976 c.435C>T synonymous_variant 0.92 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 1.0 pyrazinamide
rpsA 1833985 c.444G>T synonymous_variant 0.93 pyrazinamide
rpsA 1833994 c.453G>C synonymous_variant 0.93 pyrazinamide
rpsA 1833997 c.456G>T synonymous_variant 0.93 pyrazinamide
rpsA 1834000 c.459G>T synonymous_variant 0.94 pyrazinamide
rpsA 1834012 c.471G>A synonymous_variant 0.94 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.94 pyrazinamide
rpsA 1834018 c.477C>T synonymous_variant 0.94 pyrazinamide
rpsA 1834024 c.483G>C synonymous_variant 0.95 pyrazinamide
rpsA 1834034 c.493_495delATCinsGG frameshift_variant&missense_variant 0.95 pyrazinamide Uncertain significance
rpsA 1834039 c.498C>T synonymous_variant 0.94 pyrazinamide
rpsA 1834040 p.Lys167Gln missense_variant 0.94 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.95 pyrazinamide
rpsA 1834090 c.549G>T synonymous_variant 0.94 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.79 pyrazinamide
rpsA 1834105 c.564C>T synonymous_variant 0.75 pyrazinamide
rpsA 1834210 c.669C>T synonymous_variant 0.7 pyrazinamide
rpsA 1834213 c.672G>C synonymous_variant 0.7 pyrazinamide
rpsA 1834216 c.675C>T synonymous_variant 0.7 pyrazinamide
rpsA 1834219 c.678C>T synonymous_variant 0.7 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.58 pyrazinamide
rpsA 1834225 c.684C>G synonymous_variant 0.58 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.5 pyrazinamide
rpsA 1834241 c.700_702delCTGinsTA frameshift_variant&stop_gained 0.5 pyrazinamide Uncertain significance
rpsA 1834246 c.705G>C synonymous_variant 0.5 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.5 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.54 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.54 pyrazinamide
rpsA 1834273 c.732C>T synonymous_variant 0.54 pyrazinamide Not assoc w R - Interim