TB-Profiler result

Run: SRR21690362
Summary

Run ID: SRR21690362

Sample name:

Date: 2024-04-30T22:20:27.051791

Number of reads: 6555107

Percentage reads mapped: 99.92

Median coverage: 91.0

Strain: lineage1.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 0.98
lineage1.1.1 Indo-Oceanic RD239 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 rrs n.462C>T Uncertain significance Mutation from literature
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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance 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
gyrB 5908 c.669C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6112 p.Met291Ile missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 1.0 isoniazid 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
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 731747 c.-183T>C upstream_gene_variant 0.12 isoniazid
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 762185 c.2379G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
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 0.16 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.15 rifampicin
rpoC 763492 c.123G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763495 c.126G>A synonymous_variant 0.15 rifampicin
rpoC 763884 p.Ala172Val missense_variant 1.0 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 1.0 rifampicin Not assoc w R
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.12 rifampicin
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 779415 c.-935C>T upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
rplC 800590 c.-219G>A upstream_gene_variant 0.96 linezolid
Rv1129c 1254543 c.-9T>G upstream_gene_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
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
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.15 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 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475401 n.1745delC non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475404 n.1747A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.66 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
inhA 1674795 c.594G>C synonymous_variant 0.11 ethionamide
isoniazid
rpsA 1833661 c.120A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833703 c.162C>T synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1833817 c.276C>T synonymous_variant 0.95 pyrazinamide Not assoc w R - Interim
rpsA 1833847 c.306C>G synonymous_variant 0.11 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.12 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.12 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.18 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.19 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833995 c.454C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1834021 c.480C>T synonymous_variant 0.17 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834319 p.Val260Ile missense_variant 0.99 pyrazinamide Uncertain significance
rpsA 1834414 p.His291Gln missense_variant 0.98 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 1.0 linezolid Not assoc w R
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
bacA 2062922 p.Ile603Val missense_variant 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2064948 c.-220G>C upstream_gene_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
bacA 2064972 c.-244T>C upstream_gene_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3627181 c.-568T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627182 c.-569T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrA 3627188 c.162A>G synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627209 c.-596G>A upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrA 3627221 c.129C>T synonymous_variant 0.21 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627227 c.123T>C synonymous_variant 0.21 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627233 c.-620T>C upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrB 3627236 c.-623T>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrA 3627242 c.108C>T synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627254 c.-641C>T upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrB 3627263 c.-650C>T upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627266 c.-653A>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627272 c.-659G>T upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627275 c.-662G>T upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627296 c.-683T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrA 3627299 c.49_51delTTGinsCA frameshift_variant&missense_variant 0.13 bedaquiline
rifampicin
mtrB 3627317 c.-704T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
rpoA 3878143 p.Gly122Asp missense_variant 0.11 rifampicin Uncertain significance
rpoA 3878163 c.345C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878184 c.324C>A synonymous_variant 0.12 rifampicin
rpoA 3878187 c.321C>G synonymous_variant 0.12 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoA 3878953 c.-446C>G upstream_gene_variant 0.12 rifampicin
clpC1 4038506 c.2199G>C synonymous_variant 0.11 pyrazinamide
clpC1 4038530 p.Glu725Asp missense_variant 0.12 pyrazinamide
clpC1 4038533 p.Arg724Lys missense_variant 0.12 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.11 pyrazinamide
clpC1 4038812 c.1893T>C synonymous_variant 0.11 pyrazinamide
clpC1 4038815 c.1890G>C synonymous_variant 0.11 pyrazinamide
clpC1 4038821 c.1884G>A synonymous_variant 0.11 pyrazinamide
clpC1 4039258 p.Gln483Glu missense_variant 0.13 pyrazinamide
clpC1 4039259 c.1444_1446delGAGinsAC frameshift_variant&missense_variant 0.13 pyrazinamide
clpC1 4039268 c.1437C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4039286 c.1419T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039292 c.1413C>T synonymous_variant 0.17 pyrazinamide
clpC1 4039313 c.1392C>T synonymous_variant 0.16 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4039328 p.Ala459Gly missense_variant 0.16 pyrazinamide
clpC1 4039338 p.Thr456Gln missense_variant 0.14 pyrazinamide
clpC1 4039346 c.1359G>T synonymous_variant 0.14 pyrazinamide
clpC1 4039349 c.1356C>T synonymous_variant 0.14 pyrazinamide
clpC1 4039364 c.1341C>G synonymous_variant 0.11 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embA 4246131 p.Leu967Met missense_variant 1.0 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248220 c.1707A>G synonymous_variant 0.11 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4327240 c.234C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
whiB6 4338242 p.Gln94Glu missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4338603 c.-82C>T 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 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R