TB-Profiler result

Run: ERR2229084
Summary

Run ID: ERR2229084

Sample name:

Date: 2024-04-15T06:31:47.317392

Number of reads: 1528554

Percentage reads mapped: 93.11

Median coverage: 37.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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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 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 6811 c.1572C>T synonymous_variant 0.21 levofloxacin
moxifloxacin Not assoc w R - Interim
gyrB 6841 c.1602T>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6844 c.-458T>C upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrA 6853 c.-449A>G upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrB 6856 c.1617T>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6859 c.1620T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6862 c.1623C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6868 c.-434G>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6901 c.-401G>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6904 c.-398C>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6949 c.-353A>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656423 c.1048T>C synonymous_variant 0.15 ethionamide
rpoB 760283 c.477G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760340 c.534G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760869 p.Val355Ile missense_variant 0.2 rifampicin Uncertain significance
rpoB 762014 c.2208C>T synonymous_variant 0.2 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.23 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763402 c.33C>G synonymous_variant 0.13 rifampicin
rpoC 763441 c.72C>T synonymous_variant 0.16 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763765 c.396T>C synonymous_variant 0.31 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.34 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.36 rifampicin
rpoC 763835 p.Ala156Met missense_variant 0.37 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.29 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.25 rifampicin
rpoC 763872 p.Gly168Ala missense_variant 0.21 rifampicin
rpoC 763876 p.Glu169Asp missense_variant 0.21 rifampicin
rpoC 763879 c.510A>G synonymous_variant 0.2 rifampicin
rpoC 763900 c.531G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765580 c.2211G>C synonymous_variant 0.29 rifampicin
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 1.0 streptomycin Not assoc w R
rpsL 781715 c.156T>C synonymous_variant 0.13 streptomycin
rplC 800537 c.-272C>T upstream_gene_variant 0.17 linezolid
rplC 800540 c.-269T>C upstream_gene_variant 0.17 linezolid
rplC 800546 c.-263T>G upstream_gene_variant 0.16 linezolid
rplC 800567 c.-242A>G upstream_gene_variant 0.16 linezolid
rplC 800582 c.-227C>G upstream_gene_variant 0.15 linezolid
fbiC 1303747 p.Thr273Ala missense_variant 0.94 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
fabG1 1673380 c.-60C>G upstream_gene_variant 0.43 ethionamide
isoniazid
fabG1 1673641 p.Val68Ile missense_variant 0.21 ethionamide
isoniazid
inhA 1673646 c.-556T>C upstream_gene_variant 0.21 ethionamide
isoniazid
fabG1 1673657 p.Thr73Lys missense_variant 0.22 ethionamide
isoniazid
fabG1 1673660 p.Ala74Glu missense_variant 0.22 ethionamide
isoniazid
inhA 1673664 c.-538A>C upstream_gene_variant 0.19 ethionamide
isoniazid
inhA 1673667 c.-535A>G upstream_gene_variant 0.19 ethionamide
isoniazid
inhA 1673679 c.-523T>C upstream_gene_variant 0.18 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1673685 c.-517C>T upstream_gene_variant 0.18 ethionamide
isoniazid
fabG1 1673710 p.Leu91Ile missense_variant 0.23 ethionamide
isoniazid
rpsA 1833874 c.333T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
rpsA 1834546 c.1005T>C synonymous_variant 0.32 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834618 c.1077G>C synonymous_variant 0.26 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.22 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.39 pyrazinamide
rpsA 1834684 c.1143C>T synonymous_variant 0.35 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.29 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168728 p.Gly629Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.35 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.33 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0 ethionamide Uncertain significance
rpoA 3878761 c.-254G>C upstream_gene_variant 0.19 rifampicin
rpoA 3878764 c.-257A>G upstream_gene_variant 0.18 rifampicin
rpoA 3878785 c.-278T>G upstream_gene_variant 0.17 rifampicin
rpoA 3878788 c.-281G>C upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3878806 c.-299C>G upstream_gene_variant 0.17 rifampicin
rpoA 3878809 c.-302T>C upstream_gene_variant 0.17 rifampicin
clpC1 4039097 c.1608G>C synonymous_variant 0.25 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.19 pyrazinamide
panD 4044712 c.-431C>A upstream_gene_variant 0.4 pyrazinamide
panD 4044725 c.-444C>T upstream_gene_variant 0.44 pyrazinamide
panD 4044737 c.-456T>C upstream_gene_variant 0.47 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247914 c.1401G>C synonymous_variant 0.29 ethambutol Not assoc w R - Interim
embB 4247932 c.1419C>G synonymous_variant 0.26 ethambutol
embB 4247940 p.Leu476Trp missense_variant 0.26 ethambutol
embB 4247945 c.1432T>C synonymous_variant 0.26 ethambutol
embB 4247951 p.Ser480Ala missense_variant 0.25 ethambutol
embB 4247956 c.1443G>C synonymous_variant 0.25 ethambutol Not assoc w R - Interim
embB 4247974 c.1461C>G synonymous_variant 0.16 ethambutol
embB 4248097 c.1584C>G synonymous_variant 0.16 ethambutol
embB 4248130 c.1617G>C synonymous_variant 0.15 ethambutol
embB 4248172 c.1659G>C synonymous_variant 0.17 ethambutol
embB 4248199 c.1686A>G synonymous_variant 0.14 ethambutol
embB 4248200 p.Ile563Val missense_variant 0.14 ethambutol
embB 4248205 c.1692C>G synonymous_variant 0.13 ethambutol
embB 4248206 c.1693_1695delAGCinsGT frameshift_variant&missense_variant 0.13 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R