TB-Profiler result

Run: SRR1048868
Summary

Run ID: SRR1048868

Sample name:

Date: 2024-10-05T03:30:11.001662

Number of reads: 839128

Percentage reads mapped: 23.73

Median coverage: 19.0

Strain: lineage2.2.2

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
lineage2.2.2 East-Asian (Beijing) RD105;RD207 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)
katG p.Ser140Asn Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA c.386_394delATGTGGTCG Assoc w R
c.386_394delATGTGGTCG Mutation from literature
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn 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 7581 p.Asp94Asn missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.95 ethionamide Assoc w R Alias fabG1_c.-15C>T
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)
katG 2155693 p.Ser140Asn missense_variant 0.38 isoniazid Uncertain significance Mutation from literature
pncA 2288847 c.386_394delATGTGGTCG disruptive_inframe_deletion 1.0 pyrazinamide Assoc w R
pyrazinamide Mutation from literature
gid 4408087 c.115delC frameshift_variant 0.88 streptomycin 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
gyrB 5548 c.309A>C synonymous_variant 1.0 levofloxacin
moxifloxacin
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 9065 c.1764C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
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 759960 p.Thr52Pro missense_variant 0.87 rifampicin Uncertain significance
rpoB 762917 c.3111C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.3 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.3 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.3 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.3 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764338 p.Glu323Asp missense_variant 0.25 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.32 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.32 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.31 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.34 rifampicin
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764398 c.1029G>C synonymous_variant 0.36 rifampicin
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764410 c.1041G>T synonymous_variant 0.33 rifampicin
rpoC 764428 c.1059G>T synonymous_variant 0.22 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
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 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.4 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
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 2155637 p.Leu159Ile missense_variant 0.41 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.39 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.41 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.43 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.43 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.43 isoniazid
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.36 isoniazid Not assoc w R - Interim
katG 2155704 c.408C>T synonymous_variant 0.41 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.42 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039592 c.1113G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040976 c.-272T>G upstream_gene_variant 0.95 pyrazinamide
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
ethA 4327341 p.Trp45Gly missense_variant 0.94 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
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