TB-Profiler result

Run: SRR29051043
Summary

Run ID: SRR29051043

Sample name:

Date: 2024-09-26T13:01:09.752556

Number of reads: 692545

Percentage reads mapped: 97.92

Median coverage: 20.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.99
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 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 0.38 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 5723 p.Ala162Ser missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser 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
mshA 575240 c.-108G>A upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoB 760649 c.843G>C synonymous_variant 0.3 rifampicin
rpoB 760655 c.849A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.25 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761815 p.Ala670Glu missense_variant 0.25 rifampicin
rpoB 761873 c.2067A>C synonymous_variant 0.24 rifampicin
rpoB 761885 c.2079T>C synonymous_variant 0.27 rifampicin
rpoB 761906 c.2100C>G synonymous_variant 0.24 rifampicin
rpoB 761909 c.2103T>C synonymous_variant 0.24 rifampicin
rpoB 761912 c.2106T>C synonymous_variant 0.24 rifampicin
rpoB 761915 p.Asp703Glu missense_variant 0.24 rifampicin
rpoB 761916 p.Asp704Asn missense_variant 0.24 rifampicin
rpoB 761948 c.2142G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761999 c.2193G>C synonymous_variant 0.41 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.46 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.46 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.41 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.35 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.31 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762206 c.2400C>G synonymous_variant 0.19 rifampicin
rpoC 762419 c.-951C>G upstream_gene_variant 0.2 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.23 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 762467 c.-903C>T upstream_gene_variant 0.28 rifampicin
rpoB 762488 c.2682G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762489 p.Val895Gln missense_variant 0.3 rifampicin
rpoC 763148 c.-222G>C upstream_gene_variant 0.3 rifampicin
rpoC 763158 c.-212C>T upstream_gene_variant 0.39 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 763202 c.-168A>G upstream_gene_variant 0.33 rifampicin
rpoC 763205 c.-165G>C upstream_gene_variant 0.34 rifampicin
rpoC 763206 c.-164_-162delAGTinsTCG upstream_gene_variant 0.34 rifampicin
rpoB 763214 c.3408T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 763226 c.-144A>G upstream_gene_variant 0.32 rifampicin
rpoB 763227 c.3421C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 763238 c.3432T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763253 c.-117G>C upstream_gene_variant 0.31 rifampicin
rpoC 763256 c.-114G>A upstream_gene_variant 0.29 rifampicin
rpoB 763268 c.3462C>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763441 c.72C>T synonymous_variant 0.25 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.33 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.33 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.35 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.27 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.27 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.3 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.3 rifampicin
rpoC 763792 p.Glu141Asp missense_variant 0.21 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764419 c.1050C>G synonymous_variant 0.33 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.36 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.35 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.35 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>T synonymous_variant 0.37 rifampicin
rpoC 764527 c.1158C>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.37 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764554 c.1185C>T synonymous_variant 0.36 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 764797 c.1428G>C synonymous_variant 0.38 rifampicin
rpoC 764803 c.1434C>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.4 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.32 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.24 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765541 c.2172C>G synonymous_variant 0.27 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.24 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.23 rifampicin
rpoC 765580 c.2211G>C synonymous_variant 0.23 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.38 rifampicin Uncertain significance
rpoC 765772 c.2403C>G synonymous_variant 0.43 rifampicin
rpoC 765784 c.2415C>G synonymous_variant 0.36 rifampicin
rpoC 765793 c.2424C>G synonymous_variant 0.38 rifampicin
rpoC 765796 c.2427C>T synonymous_variant 0.36 rifampicin
rpoC 765811 c.2442T>G synonymous_variant 0.41 rifampicin
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
rpsL 781877 c.318T>C synonymous_variant 0.25 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.21 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.23 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.21 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.34 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1474409 n.756_766delACCCACACGCG non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1474427 n.770A>C non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474429 n.772G>C non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474431 n.774_775delGCinsTTTGGG non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1474435 n.780_783delGAAT non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.47 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rpsA 1833940 c.399C>G synonymous_variant 0.3 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.36 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.36 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.35 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.3 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.26 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834297 c.756C>T synonymous_variant 0.26 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.26 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834339 c.798C>T synonymous_variant 0.38 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.38 pyrazinamide Not assoc w R - Interim
tsnR 1853550 c.-55_-54delCC upstream_gene_variant 1.0 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624748 p.Phe55Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038845 c.1860G>C synonymous_variant 0.29 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.38 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.35 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.37 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTG frameshift_variant&synonymous_variant 0.32 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039286 c.1419T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.2 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039328 c.1377A>C synonymous_variant 0.17 pyrazinamide
clpC1 4039331 c.1374C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039337 p.Thr456Gln missense_variant 0.2 pyrazinamide
clpC1 4039349 c.1356C>T synonymous_variant 0.2 pyrazinamide
clpC1 4039352 c.1353C>G synonymous_variant 0.21 pyrazinamide
clpC1 4039364 c.1341C>G synonymous_variant 0.21 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.21 pyrazinamide
embC 4242182 p.Ala774Ser missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338593 c.-73delT upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R