TB-Profiler result

Run: ERR11466070
Summary

Run ID: ERR11466070

Sample name:

Date: 2024-10-03T23:06:53.035560

Number of reads: 4311309

Percentage reads mapped: 99.3

Median coverage: 98.0

Strain: lineage4.3.4.1

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
lineage4.3.4.1 Euro-American (LAM) RD174 0.99
lineage4 Euro-American None 1.0
lineage4.3.4 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
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 8250 p.Glu317Gln missense_variant 0.92 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9377 c.2076A>G synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13483 p.Ala26Thr missense_variant 1.0 isoniazid Uncertain significance
rpoB 761561 c.1755C>G synonymous_variant 0.14 rifampicin
rpoB 761564 c.1758G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>T synonymous_variant 0.13 rifampicin
rpoB 761645 c.1839C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761948 c.2142G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763169 c.-201A>G upstream_gene_variant 0.12 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 765611 p.His748Tyr missense_variant 0.12 rifampicin Uncertain significance
rpoC 765904 c.2535C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765937 c.2568T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 766363 c.2994G>T synonymous_variant 0.13 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.13 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.13 rifampicin
rpoC 766390 c.3021C>T synonymous_variant 0.15 rifampicin
rpoC 766408 c.3039C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.18 rifampicin
rpoC 766435 p.Glu1022Asp missense_variant 0.2 rifampicin Uncertain significance
rpoC 766456 c.3087C>G synonymous_variant 0.17 rifampicin
rpoC 766459 c.3090G>T synonymous_variant 0.14 rifampicin
rpoC 766484 p.Val1039Ile missense_variant 0.18 rifampicin Uncertain significance
rpoC 766843 c.3474T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 1.0 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474708 n.1052dupG non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474711 n.1054_1055insA non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474715 n.1061delA non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834489 c.948T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.13 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518606 c.492G>C synonymous_variant 0.14 isoniazid
kasA 2518609 p.Met165Ile missense_variant 0.15 isoniazid
kasA 2518651 c.537C>G synonymous_variant 0.11 isoniazid
Rv2477c 2782453 c.1590C>T synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782483 c.1560G>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625867 c.747A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3877596 c.912G>C synonymous_variant 0.12 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038997 c.1708T>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4039003 p.Asn568Asp missense_variant 0.12 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039090 c.1615C>T synonymous_variant 0.14 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039145 c.1560G>T synonymous_variant 0.12 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.14 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039187 c.1518G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039243 c.1462C>T synonymous_variant 0.17 pyrazinamide
clpC1 4039991 c.714G>A synonymous_variant 0.99 pyrazinamide Not assoc w R
clpC1 4040057 c.648C>T synonymous_variant 0.14 pyrazinamide
clpC1 4040423 c.282A>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4040431 c.274T>C synonymous_variant 0.15 pyrazinamide
clpC1 4040441 c.264C>T synonymous_variant 0.17 pyrazinamide
clpC1 4040444 c.261C>G synonymous_variant 0.17 pyrazinamide
clpC1 4040450 c.255A>G synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4040456 c.249C>T synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4040459 c.246C>A synonymous_variant 0.19 pyrazinamide
clpC1 4040465 c.240T>C synonymous_variant 0.18 pyrazinamide
clpC1 4040471 c.234T>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247463 p.Ser317Cys missense_variant 0.11 ethambutol
embB 4247470 c.957T>C synonymous_variant 0.15 ethambutol
embB 4247491 c.978G>C synonymous_variant 0.12 ethambutol
embB 4247497 c.984T>C synonymous_variant 0.12 ethambutol
embB 4247500 c.987C>G synonymous_variant 0.12 ethambutol
embB 4248264 p.Phe584Ser missense_variant 0.13 ethambutol
embB 4248275 p.Thr588Ala missense_variant 0.15 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R