TB-Profiler result

Run: SRR12420587
Summary

Run ID: SRR12420587

Sample name:

Date: 2024-03-27T04:20:16.451504

Number of reads: 3456004

Percentage reads mapped: 81.2

Median coverage: 49.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 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.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
thyA c.-981_*3841del Mutation from literature
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 0.95 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.95 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
thyX 3067961 c.-16C>T upstream_gene_variant 0.93 para-aminosalicylic_acid Mutation from literature
thyA 3069838 c.-981_*3841del transcript_ablation 0.95 para-aminosalicylic_acid Mutation from literature
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
dnaA 877 c.877T>C synonymous_variant 0.12 isoniazid
gyrA 6766 c.-536G>C upstream_gene_variant 0.12 levofloxacin
moxifloxacin
gyrB 6775 c.1536G>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6776 p.Ile513Val missense_variant 0.14 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 761039 p.Leu411Phe missense_variant 0.14 rifampicin
rpoB 761057 c.1251G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.14 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.12 rifampicin
rpoB 761990 c.2184G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762209 c.2403C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 762212 c.2406G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762248 c.2442G>C synonymous_variant 0.17 rifampicin
rpoB 762254 c.2448T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762257 c.2451C>G synonymous_variant 0.16 rifampicin
rpoC 762938 c.-432G>C upstream_gene_variant 0.15 rifampicin
rpoB 762959 c.3153G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 762962 c.-408C>G upstream_gene_variant 0.15 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763504 c.135C>G synonymous_variant 0.13 rifampicin
rpoC 763507 c.138G>C synonymous_variant 0.13 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763576 c.207C>G synonymous_variant 0.24 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764227 c.858G>C synonymous_variant 0.12 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.28 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764582 p.Leu405Met missense_variant 0.12 rifampicin
rpoC 764817 p.Val483Ala missense_variant 1.0 rifampicin Uncertain significance
rpoC 767002 c.3633G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 767008 c.3639G>C synonymous_variant 0.29 rifampicin
rpoC 767014 c.3645G>C synonymous_variant 0.38 rifampicin
rpoC 767017 c.3648C>G synonymous_variant 0.31 rifampicin
rpoC 767023 p.Asp1218Glu missense_variant 0.27 rifampicin
rpoC 767044 c.3675G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 0.94 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778480 p.Met1? start_lost 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781829 c.270G>C synonymous_variant 0.15 streptomycin
rpsL 781832 c.273T>G synonymous_variant 0.2 streptomycin
rpsL 781838 c.279G>T synonymous_variant 0.27 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.19 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.18 streptomycin
rplC 800693 c.-116A>G upstream_gene_variant 0.13 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.14 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473062 n.1217T>G non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473065 n.1220C>A non_coding_transcript_exon_variant 0.55 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833721 c.180A>G synonymous_variant 0.11 pyrazinamide
rpsA 1833736 c.195C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833769 c.228C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155674 c.438G>C synonymous_variant 0.23 isoniazid
katG 2155680 c.432G>C synonymous_variant 0.22 isoniazid
katG 2156552 c.-441C>T upstream_gene_variant 1.0 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide 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
Rv2680 2996243 p.Ile47Val missense_variant 1.0 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
lpqB 3623950 p.Val321Met missense_variant 1.0 bedaquiline
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626627 c.-14A>G upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrA 3627038 c.310_312delATGinsGC frameshift_variant&missense_variant 0.11 bedaquiline
rifampicin
clpC1 4038812 c.1893T>C synonymous_variant 0.13 pyrazinamide
panD 4044240 c.42G>C synonymous_variant 0.13 pyrazinamide
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.98 ethionamide Uncertain significance
whiB6 4338594 c.-73T>G upstream_gene_variant 0.98 capreomycin
amikacin
kanamycin
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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R