TB-Profiler result

Run: ERR4872269
Summary

Run ID: ERR4872269

Sample name:

Date: 2024-04-15T09:28:20.317609

Number of reads: 1048526

Percentage reads mapped: 26.05

Median coverage: 31.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: 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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asn296His Uncertain significance Mutation from literature
pyrazinamide pncA p.Gly105Val Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA c.110delA Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid rplC p.Cys154Arg Assoc w R
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.Asp94Ala missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.98 kanamycin Assoc w R
amikacin Assoc w R
capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288928 p.Gly105Val missense_variant 1.0 pyrazinamide Assoc w R - Interim
embB 4247399 p.Asn296His missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide 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 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 762863 c.3057T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762872 p.Met1022Ile missense_variant 0.25 rifampicin Uncertain significance
rpoB 762878 p.Ile1024Met missense_variant 0.26 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 0.26 rifampicin Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.46 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.45 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.45 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.41 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.41 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.4 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.41 rifampicin
rpoC 762998 c.-372G>A upstream_gene_variant 0.4 rifampicin
rpoB 763005 p.Cys1067Val missense_variant 0.31 rifampicin
rpoB 763014 p.Met1070Leu missense_variant 0.27 rifampicin
rpoB 763017 c.3211_3213delCAGinsGA frameshift_variant&missense_variant 0.27 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764374 c.1005C>T synonymous_variant 0.17 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.2 rifampicin
rpoC 764387 c.1018T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764401 c.1032C>T synonymous_variant 0.26 rifampicin
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.28 rifampicin
rpoC 764410 c.1041G>C synonymous_variant 0.29 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066_1068delAGGinsCC frameshift_variant&missense_variant 0.29 rifampicin
rpoC 764443 p.Ile358Met missense_variant 0.27 rifampicin
rpoC 764446 p.Asp359Glu missense_variant 0.26 rifampicin
rpoC 764450 c.1081_1083delGGTinsCG frameshift_variant&missense_variant 0.27 rifampicin
rpoC 764461 p.Glu364Asp missense_variant 0.27 rifampicin
rpoC 764468 p.Val367Ile missense_variant 0.28 rifampicin
rpoC 764471 p.Asn368Arg missense_variant 0.27 rifampicin
rpoC 764479 c.1110G>A synonymous_variant 0.28 rifampicin
rpoC 764500 c.1131C>G synonymous_variant 0.23 rifampicin
rpoC 764503 c.1134G>C synonymous_variant 0.21 rifampicin
rpoC 764509 c.1140G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764605 c.1236G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.34 rifampicin
rpoC 764623 c.1254C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764660 p.Val431Thr missense_variant 0.3 rifampicin
rpoC 764665 c.1296C>G synonymous_variant 0.31 rifampicin
rpoC 764668 c.1299C>A synonymous_variant 0.28 rifampicin
rpoC 764672 c.1303_1305delCAGinsGA frameshift_variant&missense_variant 0.28 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764687 p.Gln440Glu missense_variant 0.26 rifampicin
rpoC 764695 c.1326T>C synonymous_variant 0.28 rifampicin
rpoC 764705 p.Leu446Lys missense_variant 0.27 rifampicin
rpoC 764840 p.Ile491Val missense_variant 1.0 rifampicin Uncertain significance
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
mmpR5 779161 p.Thr58Pro missense_variant 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
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 1472344 n.499C>T non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472349 n.504A>T non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472390 n.545T>C non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.75 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 0.75 capreomycin
linezolid
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.67 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.66 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476521 n.2864C>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476525 n.2868A>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>G non_coding_transcript_exon_variant 0.25 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
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
Rv2752c 3066058 p.Cys45Phe missense_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086731 c.-89A>G upstream_gene_variant 1.0 cycloserine
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
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
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
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 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