TB-Profiler result

Run: SRR7070571
Summary

Run ID: SRR7070571

Sample name:

Date: 2024-05-20T09:30:31.796871

Number of reads: 2490388

Percentage reads mapped: 82.97

Median coverage: 75.5

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 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
dnaA 94 p.Ser32Gly missense_variant 0.99 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin 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 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
nusG 734202 c.-52G>C upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.98 rifampicin Not assoc w R
rpoC 763666 c.297G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>T synonymous_variant 0.11 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763718 p.Leu117Val missense_variant 0.11 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.11 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
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 isoniazid Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
levofloxacin Not assoc w R
fbiC 1303668 c.738C>A synonymous_variant 1.0 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 0.98 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.18 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.18 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin
capreomycin Uncertain significance
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.16 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.22 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin
capreomycin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.3 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.4 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.52 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.51 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Not assoc w R
capreomycin Not assoc w R
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.47 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.57 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.57 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.54 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin
capreomycin Uncertain significance
rrs 1473288 n.1443_1455delCTCGGGAGGGAGCinsGCGTTTGCGGGGGGAGT non_coding_transcript_exon_variant 0.54 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.49 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrl 1475610 n.1953G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.39 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476534 n.2878_2879delGG non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476540 n.2883_2885delCCTinsGGGCC non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
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
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 kanamycin Not assoc w R
moxifloxacin Not assoc w R
amikacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R - Interim
ethambutol Not assoc w R
levofloxacin 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
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4268003 c.834G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
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