TB-Profiler result

Run: ERR2517489
Summary

Run ID: ERR2517489

Sample name:

Date: 2024-04-16T07:02:14.241821

Number of reads: 4877619

Percentage reads mapped: 90.82

Median coverage: 130.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.98
lineage4.1.2 Euro-American None 0.99
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.98
lineage4 Euro-American None 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
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 7799 c.498A>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491542 c.760T>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491547 c.765A>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491550 c.768T>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491591 p.Lys270Met missense_variant 0.92 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.94 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.93 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.99 rifampicin Not assoc w R
rpoB 760430 c.624T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760522 p.Ser239Asn missense_variant 0.16 rifampicin Uncertain significance
rpoB 760532 c.726T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760533 p.Val243Thr missense_variant 0.14 rifampicin
rpoB 760547 c.741G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760563 p.Arg253Met missense_variant 0.14 rifampicin Uncertain significance
rpoB 760591 p.Val262Ala missense_variant 0.15 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760634 c.828T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.14 rifampicin
rpoB 760683 c.877T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760970 c.1164G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.14 rifampicin
rpoB 763085 c.3279C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763744 c.375G>C synonymous_variant 0.14 rifampicin
rpoC 764530 c.1161C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.14 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.15 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.99 rifampicin Not assoc w R
rpoC 765556 c.2187G>C synonymous_variant 0.14 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.14 rifampicin
rpoC 765578 c.2209C>T synonymous_variant 0.15 rifampicin
rpoC 765583 c.2214G>T synonymous_variant 0.15 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.15 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.14 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.14 rifampicin
rpoC 766972 c.3603G>C synonymous_variant 0.16 rifampicin
rpoC 766978 c.3609C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAC frameshift_variant&missense_variant 0.16 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.19 rifampicin
rpoC 767074 c.3705T>C synonymous_variant 0.21 rifampicin
rpoC 767098 c.3729T>C 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303920 c.990C>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303923 c.993C>T synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303929 c.999G>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1304817 c.1887T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304853 c.1923C>G synonymous_variant 0.25 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.21 capreomycin
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 0.18 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475271 n.1614A>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475273 n.1616T>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.15 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 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833838 c.297G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.15 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834261 c.720A>C synonymous_variant 0.14 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.14 pyrazinamide
tsnR 1853361 c.-245T>C upstream_gene_variant 0.14 linezolid
tsnR 1853370 c.-236_-234delGCAinsTG upstream_gene_variant 0.14 linezolid
tsnR 1853384 c.-222G>C upstream_gene_variant 0.14 linezolid
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 0.14 linezolid
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 2154907 p.Glu402Ala missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2517947 c.-168C>T upstream_gene_variant 0.13 isoniazid
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
kasA 2518816 c.702C>A synonymous_variant 0.13 isoniazid
Rv2477c 2783040 p.Ala335Thr missense_variant 0.16 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.19 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.25 capreomycin Uncertain significance
thyA 3073977 c.495A>G synonymous_variant 0.16 para-aminosalicylic_acid
thyA 3074001 c.471C>G synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3074004 c.468T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3074037 c.435C>G synonymous_variant 0.13 para-aminosalicylic_acid
ald 3086767 c.-53A>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625762 c.852A>G synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625797 p.Val273Met missense_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 1.0 bedaquiline
rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.14 rifampicin
rpoA 3878396 c.112C>T synonymous_variant 0.15 rifampicin
rpoA 3878436 c.72A>G synonymous_variant 0.15 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.14 rifampicin
rpoA 3878454 c.54A>C synonymous_variant 0.14 rifampicin
rpoA 3878472 p.Asp12Glu missense_variant 0.14 rifampicin
rpoA 3879151 c.-644C>T upstream_gene_variant 0.94 rifampicin
clpC1 4038755 c.1950G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4038953 c.1752A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039682 c.1023C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039685 c.1020C>T synonymous_variant 0.14 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 0.99 ethambutol Not assoc w R
embC 4241137 c.1275G>C synonymous_variant 0.16 ethambutol
embC 4241140 c.1278A>G synonymous_variant 0.16 ethambutol Not assoc w R - Interim
embC 4241141 p.Ile427Val missense_variant 0.16 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4248070 c.1557T>C synonymous_variant 0.13 ethambutol
ubiA 4269919 c.-86T>G upstream_gene_variant 0.98 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
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin