TB-Profiler result

Run: SRR13861611
Summary

Run ID: SRR13861611

Sample name:

Date: 2024-04-15T00:41:37.749225

Number of reads: 1012428

Percentage reads mapped: 16.89

Median coverage: 33.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.98
lineage4.9 Euro-American (H37Rv-like) None 0.99
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 fbiC c.1039_1041delGTTinsAC Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiB c.743delC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1303969 c.1039_1041delGTTinsAC frameshift_variant&missense_variant 0.21 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiB 3642276 c.743delC frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 8099 c.798T>C synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8111 c.810G>C synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8156 c.855T>C synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 8168 c.867A>G synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 8471 c.1170T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
mshA 575623 c.276C>G synonymous_variant 0.14 ethionamide
isoniazid
mshA 575659 c.312A>G synonymous_variant 0.17 ethionamide
isoniazid
mshA 575752 c.405G>A synonymous_variant 0.2 ethionamide
isoniazid Not assoc w R - Interim
mshA 575767 c.420G>A synonymous_variant 0.18 ethionamide
isoniazid
Rv0565c 656172 p.Lys433Asn missense_variant 1.0 ethionamide
nusG 733874 c.-379delC upstream_gene_variant 1.0 rifampicin
nusG 734570 p.Pro106His missense_variant 0.89 rifampicin
rpoC 762698 c.-672C>T upstream_gene_variant 1.0 rifampicin
rpoB 762958 p.Leu1051Pro missense_variant 0.85 rifampicin
rpoC 765835 c.2466C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.17 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.17 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
fbiC 1302962 p.Ala11Gly missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1303706 p.Leu259Arg missense_variant 0.9 clofazimine
pretomanid
delamanid
fbiC 1303836 c.906G>C synonymous_variant 0.21 clofazimine
pretomanid
delamanid
fbiC 1303845 c.915C>G synonymous_variant 0.21 clofazimine
pretomanid
delamanid
fbiC 1303846 p.Phe306Val missense_variant 0.21 clofazimine
pretomanid
delamanid
fbiC 1303854 c.924T>C synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303860 c.930A>C synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1303881 c.951G>C synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1303884 c.954T>G synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1303911 c.981G>C synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1303914 c.984C>G synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303920 c.990C>G synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1303923 c.993C>T synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1303929 c.999G>C synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1303947 c.1017T>C synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303948 p.Gly340Arg missense_variant 0.21 clofazimine
pretomanid
delamanid
fbiC 1303973 p.Gly348Ala missense_variant 0.21 clofazimine
pretomanid
delamanid
fbiC 1304001 c.1071C>G synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1304008 c.1078T>C synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1305384 c.2454G>T synonymous_variant 0.97 clofazimine
pretomanid
delamanid
sigE 1364465 p.Val18Gly missense_variant 1.0 pyrazinamide
Rv1258c 1406724 p.Gln206Leu missense_variant 1.0 streptomycin
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416800 p.Ala183Gly missense_variant 1.0 ethambutol
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.66 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
fabG1 1673153 c.-287C>G upstream_gene_variant 1.0 ethionamide
isoniazid
rpsA 1833555 p.Thr5Ser missense_variant 0.96 pyrazinamide
rpsA 1834073 p.Lys178* stop_gained 0.94 pyrazinamide Uncertain significance
rpsA 1834666 c.1125G>C synonymous_variant 0.23 pyrazinamide
rpsA 1834669 c.1128G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834688 c.1147_1149delAGTinsTCC synonymous_variant 0.23 pyrazinamide
tsnR 1853807 p.Val68Leu missense_variant 1.0 linezolid
bacA 2064191 p.Thr180Ala missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
PPE35 2167669 p.Phe982Leu missense_variant 1.0 pyrazinamide
kasA 2518621 c.507G>A synonymous_variant 0.15 isoniazid
Rv2681 2996984 c.246C>G synonymous_variant 1.0 capreomycin
Rv2681 2997866 p.Asp376Glu missense_variant 1.0 capreomycin
Rv2752c 3066234 c.-43G>A upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067718 c.228C>G synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067721 c.225T>C synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067724 c.222G>A synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067727 c.219A>C synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067739 c.207T>C synonymous_variant 0.21 para-aminosalicylic_acid
thyX 3067742 c.204A>C synonymous_variant 0.21 para-aminosalicylic_acid
thyX 3067761 p.Arg62Lys missense_variant 0.26 para-aminosalicylic_acid
thyX 3067765 p.Leu61Ile missense_variant 0.21 para-aminosalicylic_acid
thyX 3067781 c.165C>G synonymous_variant 0.22 para-aminosalicylic_acid
thyX 3067787 c.159G>A synonymous_variant 0.28 para-aminosalicylic_acid
lpqB 3624242 c.669A>C synonymous_variant 1.0 bedaquiline
rifampicin
mtrB 3625797 p.Val273Met missense_variant 0.19 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625806 c.808A>C synonymous_variant 0.21 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625837 c.777C>G synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877818 c.690A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3878111 p.Lys133Gln missense_variant 0.92 rifampicin
clpC1 4039946 c.759A>T synonymous_variant 0.16 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.16 pyrazinamide
embA 4242703 c.-530C>T upstream_gene_variant 1.0 ethambutol
embB 4249144 c.2631G>C synonymous_variant 1.0 ethambutol