TB-Profiler result

Run: ERR11465333
Summary

Run ID: ERR11465333

Sample name:

Date: 2024-04-15T23:18:14.801464

Number of reads: 4717074

Percentage reads mapped: 99.5

Median coverage: 110.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 1.0
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
capreomycin
kanamycin
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
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
gyrB 6140 p.Val301Leu missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761195 c.1389G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761201 c.1395G>A synonymous_variant 0.13 rifampicin
rpoB 762923 c.3117C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.11 rifampicin
rpoC 764134 c.765C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 765871 c.2502T>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 766607 c.3238_3240delATCinsCG frameshift_variant&missense_variant 0.11 rifampicin
rpoC 766774 c.3405T>C synonymous_variant 0.12 rifampicin
rpoC 767002 c.3633G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 0.98 streptomycin Not assoc w R
rpsL 781658 c.99A>G synonymous_variant 0.11 streptomycin
rpsL 781682 c.123T>C synonymous_variant 0.14 streptomycin
rpsL 781700 c.141G>C synonymous_variant 0.16 streptomycin
rpsL 781706 c.147T>G synonymous_variant 0.14 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.15 streptomycin
rpsL 781718 c.159C>G synonymous_variant 0.14 streptomycin
rpsL 781721 c.162C>T synonymous_variant 0.15 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.14 streptomycin
rpsL 781733 c.174G>C synonymous_variant 0.15 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.15 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.13 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.11 streptomycin
rpsL 781793 c.234G>C synonymous_variant 0.12 streptomycin
rpsL 781802 c.243G>C synonymous_variant 0.11 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.17 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1473757 n.100T>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475555 n.1898T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833859 c.318C>G synonymous_variant 0.11 pyrazinamide
rpsA 1833871 c.330G>A synonymous_variant 0.14 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833952 c.411C>T synonymous_variant 0.13 pyrazinamide
rpsA 1834093 c.552G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834279 c.738C>T synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834340 p.Met267Leu missense_variant 0.12 pyrazinamide Uncertain significance
rpsA 1834361 c.820T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834369 c.828C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834375 c.834G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834378 c.837T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834451 c.910T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834591 c.1050C>T synonymous_variant 0.16 pyrazinamide
rpsA 1834597 c.1056C>T synonymous_variant 0.14 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518864 c.750G>C synonymous_variant 0.12 isoniazid
thyX 3067248 p.Thr233Ile missense_variant 1.0 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038878 c.1827A>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4038923 c.1782A>G synonymous_variant 0.1 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038941 c.1764G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.11 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.11 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4038995 c.1708_1710delTTGinsCC frameshift_variant&missense_variant 0.15 pyrazinamide
clpC1 4039004 c.1701C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.12 pyrazinamide
clpC1 4039046 c.1659C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039064 c.1641C>T synonymous_variant 0.18 pyrazinamide
clpC1 4039067 c.1638G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039082 c.1623C>T synonymous_variant 0.12 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039091 c.1614G>T synonymous_variant 0.13 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039118 c.1587C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039121 c.1584T>G synonymous_variant 0.15 pyrazinamide
clpC1 4039133 c.1572C>G synonymous_variant 0.1 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.13 pyrazinamide
clpC1 4039172 c.1533A>G synonymous_variant 0.11 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.11 pyrazinamide
clpC1 4039199 c.1506C>G synonymous_variant 0.12 pyrazinamide
clpC1 4039239 p.Gly489Ala missense_variant 0.16 pyrazinamide
clpC1 4039244 c.1461G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039793 c.912C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039817 c.888A>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039820 c.885T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R