TB-Profiler result

Run: ERR4820043
Summary

Run ID: ERR4820043

Sample name:

Date: 2024-04-16T04:59:39.095427

Number of reads: 2528389

Percentage reads mapped: 85.0

Median coverage: 58.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 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 6061 c.822C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7394 c.93T>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7397 c.96G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7553 c.252C>T synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7559 c.258G>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7565 c.264C>T synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7574 c.273G>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7589 c.288G>C synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.97 rifampicin Not assoc w R
rpoB 761084 c.1278C>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761198 c.1392G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761219 c.1413G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761234 c.1428G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762038 c.2232C>T synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762236 c.2430G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762275 c.2469C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762284 c.2478G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762296 c.2490G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763082 c.3276C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763088 c.3282C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763492 c.123G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763531 c.162G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764530 c.1161C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764534 c.1165C>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764542 c.1173C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764545 c.1176C>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764560 c.1191T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764692 c.1323C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 764810 p.Pro481Ala missense_variant 0.14 rifampicin Uncertain significance
rpoC 764815 c.1446A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764869 c.1500C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764887 c.1518G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.11 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765409 c.2040T>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 765421 c.2052C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 767080 c.3711G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767098 c.3729T>C synonymous_variant 0.16 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
mmpL5 777404 c.1077C>T synonymous_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473812 n.155G>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1473814 n.157A>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rpsA 1833874 c.333T>G synonymous_variant 0.11 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.11 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.12 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.16 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 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.26 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.13 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448432 c.-72C>A upstream_gene_variant 1.0 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878193 c.315T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoA 3878196 p.Glu104Ala missense_variant 0.11 rifampicin Uncertain significance
rpoA 3878217 c.291A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878271 c.237T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
clpC1 4039661 c.1044T>C synonymous_variant 0.12 pyrazinamide
clpC1 4039682 c.1023C>G synonymous_variant 0.1 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_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
whiB6 4338787 c.-266G>A upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin