TB-Profiler result

Run: SRR15014682
Summary

Run ID: SRR15014682

Sample name:

Date: 2024-10-04T01:00:00.324608

Number of reads: 1789606

Percentage reads mapped: 99.07

Median coverage: 94.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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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 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Val1Ala Mutation from literature
ethambutol embB p.Met306Leu Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin Assoc w R
katG 2156110 p.Val1Ala missense_variant 1.0 isoniazid Mutation from literature
embB 4247429 p.Met306Leu missense_variant 0.64 ethambutol 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
gyrA 7484 c.183T>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 7490 c.189C>A synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 7496 c.195C>G synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7523 c.222C>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7526 c.225G>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7556 c.255C>T synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7592 c.291G>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7595 c.294C>G synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7601 c.300C>G synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7631 c.330G>T synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7637 c.336C>T synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7652 c.351C>T synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 7658 c.357A>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 7664 c.363T>C synonymous_variant 0.12 levofloxacin
moxifloxacin
mshA 576347 p.Thr334Ala missense_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
rpoC 766540 p.Asp1057Glu missense_variant 0.12 rifampicin
rpoC 766570 c.3201T>C synonymous_variant 0.12 rifampicin
rpoC 766573 c.3204T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 766585 c.3216T>C synonymous_variant 0.12 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.11 rifampicin
rpoC 766942 c.3573C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766945 c.3576A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.15 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767059 c.3690T>G synonymous_variant 0.11 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223491 c.-327C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2289652 c.-411C>A upstream_gene_variant 1.0 pyrazinamide
Rv2477c 2782717 c.1326G>A synonymous_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
rpoA 3878061 c.447G>C synonymous_variant 0.12 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.11 rifampicin
rpoA 3878082 c.426T>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoA 3878085 c.423G>A synonymous_variant 0.12 rifampicin
rpoA 3878106 c.402G>C synonymous_variant 0.11 rifampicin
rpoA 3878143 p.Gly122Asp missense_variant 0.11 rifampicin Uncertain significance
rpoA 3879154 c.-647T>C upstream_gene_variant 0.11 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.13 rifampicin
rpoA 3879163 c.-656C>T upstream_gene_variant 0.13 rifampicin
rpoA 3879178 c.-671T>G upstream_gene_variant 0.11 rifampicin
rpoA 3879187 c.-680C>T upstream_gene_variant 0.12 rifampicin
rpoA 3879202 c.-695T>C upstream_gene_variant 0.12 rifampicin
rpoA 3879208 c.-701C>G upstream_gene_variant 0.12 rifampicin
clpC1 4038743 c.1962G>A synonymous_variant 0.14 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038764 c.1941C>G synonymous_variant 0.14 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038838 c.1867C>T synonymous_variant 0.18 pyrazinamide
clpC1 4038854 c.1851G>A synonymous_variant 0.17 pyrazinamide
clpC1 4038857 c.1848C>T synonymous_variant 0.17 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4038884 c.1821C>T synonymous_variant 0.19 pyrazinamide
clpC1 4038896 c.1809C>T synonymous_variant 0.2 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.19 pyrazinamide
clpC1 4038911 c.1794G>A synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4038914 c.1791G>C synonymous_variant 0.2 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTTG synonymous_variant 0.19 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.19 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.18 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.12 pyrazinamide
clpC1 4039064 c.1641C>G synonymous_variant 0.11 pyrazinamide
clpC1 4040387 c.318A>G synonymous_variant 0.13 pyrazinamide
clpC1 4040393 c.312G>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4040402 c.303C>T synonymous_variant 0.13 pyrazinamide
clpC1 4040411 c.294T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4040423 c.282A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4040431 c.274T>C synonymous_variant 0.17 pyrazinamide
clpC1 4040441 c.264C>G synonymous_variant 0.17 pyrazinamide
clpC1 4040444 c.261C>T synonymous_variant 0.18 pyrazinamide
clpC1 4040450 c.255A>G synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4040456 c.249C>T synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4040459 c.246C>G synonymous_variant 0.19 pyrazinamide
clpC1 4040471 c.234T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4040477 c.228G>T synonymous_variant 0.16 pyrazinamide
clpC1 4040480 c.225T>G synonymous_variant 0.16 pyrazinamide
clpC1 4040507 c.198C>T synonymous_variant 0.83 pyrazinamide
clpC1 4040522 c.183T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040528 c.177G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040531 c.174T>C synonymous_variant 0.15 pyrazinamide
clpC1 4040546 c.159G>A synonymous_variant 0.14 pyrazinamide
clpC1 4040551 c.154T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4040561 c.144A>G synonymous_variant 0.14 pyrazinamide
clpC1 4040567 c.138C>G synonymous_variant 0.13 pyrazinamide
clpC1 4040573 c.132T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4040582 c.123G>T synonymous_variant 0.12 pyrazinamide
clpC1 4040591 c.114C>T synonymous_variant 0.12 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R