TB-Profiler result

Run: SRR28351347
Summary

Run ID: SRR28351347

Sample name:

Date: 2024-10-05T12:11:15.876289

Number of reads: 5283385

Percentage reads mapped: 97.86

Median coverage: 158.0

Strain: lineage3

Spoligotype:

Drug-resistance: Other

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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 pncA c.421delC Assoc w R
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
pncA 2288820 c.421delC frameshift_variant 0.89 pyrazinamide 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 7433 c.132G>A synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 7442 c.141G>C synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 7460 c.159C>A synonymous_variant 0.42 levofloxacin
moxifloxacin
gyrA 7463 c.162G>C synonymous_variant 0.42 levofloxacin
moxifloxacin
gyrA 7469 c.168C>G synonymous_variant 0.45 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7472 c.171T>C synonymous_variant 0.44 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 0.47 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.45 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 0.46 levofloxacin
moxifloxacin
gyrA 7487 c.186C>G synonymous_variant 0.48 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7496 c.195C>T synonymous_variant 0.51 levofloxacin
moxifloxacin
gyrA 7523 c.222C>G synonymous_variant 0.61 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7526 c.225G>C synonymous_variant 0.61 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7532 c.231T>G synonymous_variant 0.61 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 0.59 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 0.6 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7565 c.264C>T synonymous_variant 0.62 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7592 c.291G>C synonymous_variant 0.51 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7607 c.306C>G synonymous_variant 0.41 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7619 c.318C>T synonymous_variant 0.42 levofloxacin
moxifloxacin
gyrA 7631 c.330G>C synonymous_variant 0.45 levofloxacin
moxifloxacin
gyrA 7637 c.336C>T synonymous_variant 0.42 levofloxacin
moxifloxacin
gyrA 7652 c.351C>T synonymous_variant 0.36 levofloxacin
moxifloxacin
gyrA 7658 c.357A>G synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 7664 c.363T>C synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 7670 c.369A>C synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 7671 p.Pro124Ala missense_variant 0.23 levofloxacin
moxifloxacin
gyrA 7676 c.375G>C synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 7683 c.382A>C synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 7694 c.393A>G synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 7715 c.414G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7730 p.Arg143Ser missense_variant 0.17 levofloxacin
moxifloxacin
gyrA 7763 c.462T>G synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 7793 c.492G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7799 c.498A>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7802 c.501C>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 7832 c.531G>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 7835 c.534A>G synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7841 c.540C>T synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7847 c.546G>C synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 7859 c.558A>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8579 p.Asp426Glu missense_variant 0.24 levofloxacin
moxifloxacin
gyrA 8597 c.1296C>T synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8603 c.1302A>C synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 8609 c.1308G>C synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8624 c.1323G>T synonymous_variant 0.23 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8627 c.1326C>G synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 8628 c.1327C>T synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 8633 c.1332C>T synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 8636 c.1335A>C synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8645 c.1344C>T synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8649 p.Arg450Lys missense_variant 0.19 levofloxacin
moxifloxacin
gyrA 8663 c.1362C>T synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8672 c.1371A>G synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8948 c.1647G>A synonymous_variant 0.91 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 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575692 c.345G>A synonymous_variant 0.17 isoniazid
ethionamide
mshA 575695 c.348C>G synonymous_variant 0.18 isoniazid Not assoc w R - Interim
ethionamide
mshA 575705 c.358T>C synonymous_variant 0.21 isoniazid
ethionamide
mshA 575713 c.366G>A synonymous_variant 0.27 isoniazid
ethionamide
mshA 575716 c.369C>T synonymous_variant 0.26 isoniazid
ethionamide
mshA 575734 c.387T>G synonymous_variant 0.31 isoniazid
ethionamide
mshA 575737 c.390T>C synonymous_variant 0.31 isoniazid
ethionamide
mshA 575744 p.Ala133Thr missense_variant 0.33 isoniazid Uncertain significance
ethionamide
mshA 575749 c.402C>G synonymous_variant 0.34 isoniazid
ethionamide
mshA 575756 c.409C>T synonymous_variant 0.32 isoniazid
ethionamide
mshA 575761 c.414C>G synonymous_variant 0.32 isoniazid
ethionamide
mshA 575771 p.Val142Thr missense_variant 0.33 isoniazid
ethionamide
mshA 575779 c.432A>G synonymous_variant 0.34 isoniazid
ethionamide
mshA 575782 c.435G>C synonymous_variant 0.34 isoniazid
ethionamide
mshA 575785 c.438T>C synonymous_variant 0.34 isoniazid
ethionamide
mshA 575795 p.Ile150Val missense_variant 0.34 isoniazid
ethionamide
mshA 575842 c.495G>C synonymous_variant 0.26 isoniazid
ethionamide
mshA 575843 p.Arg166Ser missense_variant 0.26 isoniazid
ethionamide
mshA 575864 c.517T>C synonymous_variant 0.17 isoniazid
ethionamide
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
nusG 734421 c.168A>C synonymous_variant 0.2 rifampicin
nusG 734424 c.171G>T synonymous_variant 0.21 rifampicin
nusG 734439 c.186C>G synonymous_variant 0.28 rifampicin
nusG 734442 c.189G>A synonymous_variant 0.27 rifampicin
nusG 734451 c.198G>C synonymous_variant 0.28 rifampicin
nusG 734454 c.201A>G synonymous_variant 0.28 rifampicin
nusG 734460 c.207G>C synonymous_variant 0.29 rifampicin
nusG 734472 c.219T>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
nusG 734475 c.222T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
nusG 734481 c.228C>T synonymous_variant 0.33 rifampicin
nusG 734499 c.246G>C synonymous_variant 0.35 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
nusG 734559 c.306T>C synonymous_variant 0.17 rifampicin
rpoB 759746 c.-61C>T upstream_gene_variant 0.99 rifampicin Not assoc w R
rpoB 760571 c.765G>C synonymous_variant 0.19 rifampicin
rpoB 760585 p.Asn260Ser missense_variant 0.25 rifampicin
rpoB 760591 p.Val262Ala missense_variant 0.26 rifampicin
rpoB 760595 c.789C>T synonymous_variant 0.25 rifampicin
rpoB 760596 p.Thr264Pro missense_variant 0.28 rifampicin
rpoB 760608 c.802C>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 760611 c.805T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760658 c.852G>A synonymous_variant 0.46 rifampicin
rpoB 760661 c.855A>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.48 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 760721 c.915C>G synonymous_variant 0.51 rifampicin
rpoB 760730 c.924T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760748 c.942C>G synonymous_variant 0.41 rifampicin
rpoB 760751 c.945G>C synonymous_variant 0.39 rifampicin
rpoB 760754 c.948G>C synonymous_variant 0.38 rifampicin
rpoB 760755 p.His317Asn missense_variant 0.38 rifampicin
rpoB 760759 p.Val318Ala missense_variant 0.41 rifampicin
rpoB 760764 p.Glu320Gln missense_variant 0.4 rifampicin
rpoB 760769 c.963C>G synonymous_variant 0.42 rifampicin
rpoB 760793 c.987A>G synonymous_variant 0.4 rifampicin
rpoB 760805 c.999G>C synonymous_variant 0.39 rifampicin
rpoB 760817 c.1011A>G synonymous_variant 0.34 rifampicin
rpoB 760820 c.1014T>C synonymous_variant 0.34 rifampicin
rpoB 760826 c.1020C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 760830 c.1024T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 760841 c.1035T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 760859 c.1053T>C synonymous_variant 0.23 rifampicin
rpoB 760862 c.1056G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760877 c.1071G>C synonymous_variant 0.2 rifampicin
rpoB 760883 c.1077G>C synonymous_variant 0.16 rifampicin
rpoB 760886 c.1080A>G synonymous_variant 0.16 rifampicin
rpoB 760887 p.Thr361Val missense_variant 0.16 rifampicin Uncertain significance
rpoB 761217 p.Pro471Ala missense_variant 0.3 rifampicin
rpoB 761220 c.1414_1416delTCGinsAGC synonymous_variant 0.3 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761264 c.1458C>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761300 c.1494G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761318 c.1512G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761600 c.1794T>C synonymous_variant 0.15 rifampicin
rpoB 761606 c.1800C>G synonymous_variant 0.2 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.25 rifampicin
rpoB 761666 c.1860G>C synonymous_variant 0.3 rifampicin
rpoB 761669 c.1863C>T synonymous_variant 0.32 rifampicin
rpoB 761675 c.1869G>C synonymous_variant 0.34 rifampicin
rpoB 761687 c.1881C>T synonymous_variant 0.34 rifampicin
rpoB 761690 c.1884G>C synonymous_variant 0.34 rifampicin
rpoB 761693 c.1887G>C synonymous_variant 0.34 rifampicin
rpoB 761708 c.1902C>T synonymous_variant 0.39 rifampicin
rpoB 761718 p.Ala638Ser missense_variant 0.37 rifampicin
rpoB 761723 p.GluSer640LysAla missense_variant 0.38 rifampicin
rpoB 761736 p.Ile644Val missense_variant 0.31 rifampicin Uncertain significance
rpoB 761747 c.1941G>C synonymous_variant 0.28 rifampicin
rpoB 761765 c.1959T>C synonymous_variant 0.22 rifampicin
rpoB 761772 p.His656Ala missense_variant 0.21 rifampicin
rpoB 761778 p.Asn658Asp missense_variant 0.19 rifampicin
rpoB 761791 p.Arg662His missense_variant 0.2 rifampicin
rpoB 761813 c.2007T>C synonymous_variant 0.17 rifampicin
rpoB 761816 c.2010C>G synonymous_variant 0.18 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 763831 c.462A>G synonymous_variant 0.21 rifampicin
rpoC 763837 c.468G>C synonymous_variant 0.25 rifampicin
rpoC 763840 c.471G>C synonymous_variant 0.28 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.32 rifampicin
rpoC 763861 c.492C>T synonymous_variant 0.31 rifampicin
rpoC 763871 p.Gly168Ser missense_variant 0.3 rifampicin
rpoC 763876 p.Glu169Asp missense_variant 0.3 rifampicin
rpoC 763879 c.510A>G synonymous_variant 0.3 rifampicin
rpoC 763891 c.522G>A synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 763894 c.525A>G synonymous_variant 0.32 rifampicin
rpoC 763900 c.531G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763921 c.552G>C synonymous_variant 0.33 rifampicin
rpoC 763924 c.555G>A synonymous_variant 0.32 rifampicin
rpoC 763933 c.564C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763940 p.Ala191Ser missense_variant 0.24 rifampicin Uncertain significance
rpoC 763945 c.576T>C synonymous_variant 0.21 rifampicin
rpoC 763947 p.Ala193Val missense_variant 0.21 rifampicin Uncertain significance
rpoC 763951 c.582G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763960 c.591T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767008 c.3639G>A synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 767020 c.3651C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 767023 c.3654C>T synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 767059 c.3690T>C synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 767098 c.3729T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 767104 c.3735C>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 767105 p.Asn1246Gln missense_variant 0.51 rifampicin Uncertain significance
rpoC 767158 c.3789T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 767162 p.Asn1265Ala missense_variant 0.28 rifampicin
rpoC 767167 c.3798C>T synonymous_variant 0.27 rifampicin
rpoC 767174 p.Asn1269Asp missense_variant 0.26 rifampicin
rpoC 767180 p.Ala1271Gln missense_variant 0.25 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 767197 c.3828G>A synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 767200 c.3831G>A synonymous_variant 0.2 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
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
fbiC 1305150 c.2220C>G synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1305249 c.2319G>C synonymous_variant 0.16 pretomanid
delamanid
clofazimine
Rv1258c 1407108 p.Ala78Val missense_variant 0.83 streptomycin
pyrazinamide
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472848 n.1003T>A non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rpsA 1834732 c.1191T>C synonymous_variant 0.47 pyrazinamide
rpsA 1834738 c.1197A>G synonymous_variant 0.46 pyrazinamide
rpsA 1834753 c.1212T>C synonymous_variant 0.46 pyrazinamide
rpsA 1834756 c.1215G>A synonymous_variant 0.45 pyrazinamide
rpsA 1834759 c.1218A>C synonymous_variant 0.45 pyrazinamide
rpsA 1834765 p.Glu408Asp missense_variant 0.46 pyrazinamide
rpsA 1834774 c.1233C>T synonymous_variant 0.42 pyrazinamide
rpsA 1834776 p.Ala412Glu missense_variant 0.41 pyrazinamide
rpsA 1834780 c.1239A>G synonymous_variant 0.42 pyrazinamide
rpsA 1834786 c.1245A>G synonymous_variant 0.43 pyrazinamide
rpsA 1834789 c.1248T>C synonymous_variant 0.43 pyrazinamide
rpsA 1834792 c.1251G>C synonymous_variant 0.44 pyrazinamide
rpsA 1834829 p.Ala430Thr missense_variant 0.39 pyrazinamide
rpsA 1834852 c.1311C>G synonymous_variant 0.23 pyrazinamide
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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.98 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
kasA 2517941 c.-174C>G upstream_gene_variant 0.19 isoniazid
kasA 2517959 c.-156C>T upstream_gene_variant 0.19 isoniazid
kasA 2517962 c.-153C>G upstream_gene_variant 0.19 isoniazid
kasA 2517968 c.-147T>C upstream_gene_variant 0.18 isoniazid
kasA 2517974 c.-141T>C upstream_gene_variant 0.18 isoniazid
kasA 2517989 c.-126T>G upstream_gene_variant 0.16 isoniazid
kasA 2517993 c.-122G>T upstream_gene_variant 0.16 isoniazid
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
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
thyX 3067709 p.Ser79Thr missense_variant 0.15 para-aminosalicylic_acid
thyX 3067712 c.234G>C synonymous_variant 0.15 para-aminosalicylic_acid
thyX 3067718 c.228C>G synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067727 c.219A>C synonymous_variant 0.16 para-aminosalicylic_acid
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
rpoA 3877728 c.780C>G synonymous_variant 0.24 rifampicin
rpoA 3877731 c.777G>T synonymous_variant 0.23 rifampicin
rpoA 3877737 c.771G>C synonymous_variant 0.25 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877770 c.735_738delGTCAinsCAGC synonymous_variant 0.35 rifampicin
rpoA 3877776 c.732T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoA 3877785 c.723C>A synonymous_variant 0.38 rifampicin
rpoA 3877803 c.705G>C synonymous_variant 0.49 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.59 rifampicin
rpoA 3877866 c.642G>C synonymous_variant 0.6 rifampicin
rpoA 3877875 c.633T>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoA 3877887 c.621G>C synonymous_variant 0.59 rifampicin
rpoA 3877893 c.615C>T synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoA 3877905 c.603A>G synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoA 3877920 c.588G>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.52 rifampicin
rpoA 3877929 c.579C>T synonymous_variant 0.54 rifampicin
rpoA 3877962 c.546G>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877971 p.Asp179Glu missense_variant 0.27 rifampicin Uncertain significance
rpoA 3877974 c.534G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877992 c.516C>G synonymous_variant 0.14 rifampicin
rpoA 3878082 c.426T>G synonymous_variant 0.87 rifampicin Not assoc w R - Interim
clpC1 4039067 c.1638G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
clpC1 4039085 c.1620A>G synonymous_variant 0.23 pyrazinamide
clpC1 4039091 c.1614G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039097 c.1608G>T synonymous_variant 0.28 pyrazinamide
clpC1 4039100 c.1605C>T synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
clpC1 4039103 c.1602T>C synonymous_variant 0.28 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.3 pyrazinamide
clpC1 4039136 c.1569C>T synonymous_variant 0.38 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.39 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.39 pyrazinamide
clpC1 4039169 c.1536A>G synonymous_variant 0.44 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.45 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.46 pyrazinamide
clpC1 4039187 c.1518G>T synonymous_variant 0.44 pyrazinamide
clpC1 4039190 c.1515C>G synonymous_variant 0.42 pyrazinamide
clpC1 4039199 c.1506C>G synonymous_variant 0.4 pyrazinamide
clpC1 4039241 c.1464G>C synonymous_variant 0.35 pyrazinamide
clpC1 4039262 c.1443C>T synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
clpC1 4039274 c.1431G>C synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
clpC1 4039277 c.1428C>G synonymous_variant 0.2 pyrazinamide
clpC1 4039280 c.1425G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039286 c.1419T>C synonymous_variant 0.2 pyrazinamide
clpC1 4039292 c.1413C>T synonymous_variant 0.2 pyrazinamide
clpC1 4039295 c.1410A>G synonymous_variant 0.2 pyrazinamide
clpC1 4039310 c.1395A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039313 c.1392C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039346 c.1359G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039352 c.1353C>G synonymous_variant 0.22 pyrazinamide
clpC1 4039361 c.1344C>A synonymous_variant 0.29 pyrazinamide
clpC1 4039382 c.1323C>G synonymous_variant 0.31 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.3 pyrazinamide
clpC1 4039394 c.1311G>C synonymous_variant 0.3 pyrazinamide
clpC1 4039397 c.1308A>G synonymous_variant 0.32 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.3 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.3 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.28 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.31 pyrazinamide
clpC1 4039442 c.1263A>G synonymous_variant 0.3 pyrazinamide
clpC1 4039454 c.1251A>T synonymous_variant 0.28 pyrazinamide
clpC1 4039463 c.1242C>G synonymous_variant 0.27 pyrazinamide
clpC1 4039466 c.1239T>C synonymous_variant 0.27 pyrazinamide
clpC1 4039469 c.1236T>C synonymous_variant 0.26 pyrazinamide
clpC1 4039481 c.1224T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039487 c.1218G>C synonymous_variant 0.24 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.97 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240819 c.957A>C synonymous_variant 0.2 ethambutol
embC 4240825 c.963G>A synonymous_variant 0.2 ethambutol
embC 4240831 c.969T>G synonymous_variant 0.19 ethambutol
embC 4240837 c.975C>T synonymous_variant 0.19 ethambutol
embC 4242075 p.Arg738Gln missense_variant 0.99 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248070 c.1557T>C synonymous_variant 0.16 ethambutol
embB 4248085 c.1572T>C synonymous_variant 0.22 ethambutol
embB 4248097 c.1584C>G synonymous_variant 0.25 ethambutol
embB 4248106 c.1593C>G synonymous_variant 0.26 ethambutol
embB 4248118 c.1605T>C synonymous_variant 0.26 ethambutol
embB 4248130 c.1617G>C synonymous_variant 0.25 ethambutol
embB 4248142 c.1629T>C synonymous_variant 0.22 ethambutol
embB 4248143 p.Leu544Ile missense_variant 0.22 ethambutol
embB 4248157 c.1644A>G synonymous_variant 0.24 ethambutol Not assoc w R - Interim
embB 4248158 p.Cys549Ser missense_variant 0.23 ethambutol
embB 4248167 p.Thr552Ala missense_variant 0.23 ethambutol
embB 4248170 p.Ala553Ser missense_variant 0.22 ethambutol
embB 4248173 p.Val554Leu missense_variant 0.23 ethambutol
embB 4248199 c.1686A>G synonymous_variant 0.26 ethambutol
embB 4248200 p.Ile563Val missense_variant 0.25 ethambutol
embB 4248206 p.Ser565Gly missense_variant 0.23 ethambutol Uncertain significance
embB 4248220 c.1707A>G synonymous_variant 0.21 ethambutol Not assoc w R - Interim
embB 4248225 p.Ala571Val missense_variant 0.18 ethambutol Uncertain significance
embB 4248233 c.1720C>T synonymous_variant 0.17 ethambutol
embB 4249000 c.2487T>G synonymous_variant 0.85 ethambutol Not assoc w R - Interim
aftB 4268468 c.369G>A synonymous_variant 0.94 ethambutol
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 0.99 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R