TB-Profiler result

Run: ERR11138607
Summary

Run ID: ERR11138607

Sample name:

Date: 2024-04-15T10:54:49.160077

Number of reads: 4592906

Percentage reads mapped: 96.5

Median coverage: 105.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-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 1.0
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
gyrA 7582 p.Asp94Gly missense_variant 0.99 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.92 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
embB 4247429 p.Met306Val missense_variant 0.95 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 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9182 c.1881T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9191 c.1890G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9200 c.1899A>G synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9204 p.Ser635Thr missense_variant 0.2 levofloxacin
moxifloxacin
gyrA 9224 c.1923C>T synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 9230 c.1929T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 9233 c.1932C>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 9239 c.1938C>T synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9252 p.Val651Ile missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 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
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
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 760328 c.522G>C synonymous_variant 0.13 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760925 c.1119T>C synonymous_variant 0.12 rifampicin
rpoB 760928 c.1122G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760931 c.1125C>G synonymous_variant 0.12 rifampicin
rpoB 760934 c.1128C>T synonymous_variant 0.12 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762008 c.2202C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.14 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.14 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.12 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.12 rifampicin
rpoB 762266 c.2460T>C synonymous_variant 0.12 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 763774 c.405G>C synonymous_variant 0.12 rifampicin
rpoC 764248 c.879C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764257 c.888G>C synonymous_variant 0.14 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.13 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.14 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.14 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765700 c.2331T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765850 c.2481G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.12 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.15 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.15 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.14 rifampicin
rpoC 766861 c.3492G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.13 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.17 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.16 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGC synonymous_variant 0.13 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.13 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 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
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 781682 c.123T>C synonymous_variant 0.12 streptomycin
rpsL 781700 c.141G>C synonymous_variant 0.13 streptomycin
rpsL 781703 c.144G>T synonymous_variant 0.12 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.15 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.15 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.15 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.15 streptomycin
rpsL 781748 c.189C>G synonymous_variant 0.14 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.14 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.13 streptomycin
rpsL 781772 c.213C>A synonymous_variant 0.12 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.15 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.14 streptomycin
rplC 800582 c.-227C>G upstream_gene_variant 0.13 linezolid
rplC 800612 c.-197A>G upstream_gene_variant 0.12 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.12 linezolid
Rv1129c 1254111 p.Thr142Pro missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
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 1473105 n.1260G>A non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
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 2155678 p.Arg145Leu missense_variant 0.99 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168757 p.Gln619Arg missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
lpqB 3624955 c.-45C>T upstream_gene_variant 0.32 bedaquiline
rifampicin
mtrB 3624989 p.Ala542Val missense_variant 1.0 bedaquiline
rifampicin
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
rpoA 3877949 p.Thr187Ala missense_variant 0.96 rifampicin Uncertain significance
rpoA 3878436 c.72A>G synonymous_variant 0.12 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.12 rifampicin
rpoA 3879005 c.-499_-498delAAinsCG upstream_gene_variant 0.12 rifampicin
rpoA 3879013 c.-506A>G upstream_gene_variant 0.13 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.11 rifampicin
rpoA 3879178 c.-671T>C upstream_gene_variant 0.12 rifampicin
clpC1 4038860 c.1845G>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4245725 c.-789A>G upstream_gene_variant 0.14 ethambutol
embB 4245726 c.-788T>C upstream_gene_variant 0.14 ethambutol
embB 4245737 c.-777A>C upstream_gene_variant 0.13 ethambutol
embB 4245740 c.-774T>C upstream_gene_variant 0.13 ethambutol
embB 4247491 c.978G>C synonymous_variant 0.12 ethambutol
embB 4247539 c.1026T>C synonymous_variant 0.12 ethambutol
embB 4248157 c.1644A>G synonymous_variant 0.12 ethambutol Not assoc w R - Interim
embB 4248304 c.1791G>C synonymous_variant 0.14 ethambutol
embB 4248316 c.1803C>G synonymous_variant 0.12 ethambutol
embB 4248319 c.1806A>G synonymous_variant 0.13 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.96 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
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