TB-Profiler result

Run: SRR6046863
Summary

Run ID: SRR6046863

Sample name:

Date: 2024-03-26T19:39:34.869900

Number of reads: 817926

Percentage reads mapped: 31.58

Median coverage: 24.0

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.99
lineage1.1 Indo-Oceanic RD239 0.99
lineage1 Indo-Oceanic RD239 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
gyrB 6112 p.Met291Ile missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 6760 c.-542G>C upstream_gene_variant 0.27 levofloxacin
moxifloxacin
gyrA 6764 c.-538C>T upstream_gene_variant 0.29 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 8452 p.Ala384Val missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_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
Rv0010c 13298 p.Ile87Met missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid 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 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 761564 c.1758G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761612 c.1806G>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.29 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 0.24 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.24 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.83 rifampicin Not assoc w R
rpoC 763886 c.517_519delCGGinsAC frameshift_variant&missense_variant 0.83 rifampicin
rpoC 764461 c.1092A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764506 c.1137C>T synonymous_variant 0.23 rifampicin
rpoC 764527 c.1158C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764530 c.1161C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>A synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>A synonymous_variant 0.25 rifampicin
rpoC 764554 c.1185C>T synonymous_variant 0.28 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.33 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.45 rifampicin
rpoC 764602 c.1233C>T synonymous_variant 0.45 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>T synonymous_variant 0.37 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764810 c.1441_1443delCCCinsGT frameshift_variant&missense_variant 0.14 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.15 rifampicin
rpoC 765171 p.Pro601Leu missense_variant 1.0 rifampicin Not assoc w R
rpoC 767188 c.3819G>A synonymous_variant 0.21 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767197 c.3828G>A synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767203 c.3834C>G synonymous_variant 0.18 rifampicin
rpoC 767206 c.3837C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767209 c.3840T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767212 c.3843G>C synonymous_variant 0.17 rifampicin
rpoC 767221 c.3852C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767230 c.3861G>T synonymous_variant 0.18 rifampicin
rpoC 767233 c.3864T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
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 776395 p.Phe696Leu missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid 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
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.62 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 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474074 n.417C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474089 n.432C>T non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1474093 n.436G>A non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1474100 n.443C>T non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1474103 n.446A>C non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1474106 n.449_450insCT non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1474109 n.453_454delAT non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1474181 n.524_525insT non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1474185 n.529delA non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833748 c.207C>G synonymous_variant 0.21 pyrazinamide
rpsA 1833751 c.210C>T synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1833760 c.219C>T synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1833787 c.246C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.2 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.23 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.19 pyrazinamide
rpsA 1833829 c.288A>G synonymous_variant 0.2 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.18 pyrazinamide
rpsA 1833838 c.297G>T synonymous_variant 0.18 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.2 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.21 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.16 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.25 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.25 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.22 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.23 pyrazinamide
rpsA 1834297 c.756C>T synonymous_variant 0.21 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.2 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834339 c.798C>T synonymous_variant 0.17 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>A synonymous_variant 0.25 pyrazinamide
rpsA 1834378 c.837T>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>T synonymous_variant 0.22 pyrazinamide
rpsA 1834405 c.864C>T synonymous_variant 0.21 pyrazinamide
rpsA 1834408 c.867C>T synonymous_variant 0.21 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.19 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 1.0 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin 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
PPE35 2167983 p.Gly877Asp missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169194 c.1419C>A synonymous_variant 1.0 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 1.0 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625735 c.879C>A synonymous_variant 0.25 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625744 c.870G>A synonymous_variant 0.25 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625755 p.Ala287Thr missense_variant 0.28 bedaquiline
rifampicin Uncertain significance
mtrB 3625761 p.Gln285Glu missense_variant 0.27 bedaquiline
rifampicin Uncertain significance
mtrB 3625762 c.852A>G synonymous_variant 0.26 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625765 c.849C>G synonymous_variant 0.29 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625768 c.-858G>C upstream_gene_variant 0.3 bedaquiline
rifampicin
mtrB 3625774 c.840G>A synonymous_variant 0.3 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625792 c.822G>T synonymous_variant 0.32 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625801 c.-891G>C upstream_gene_variant 0.27 bedaquiline
rifampicin
mtrB 3625806 c.808A>C synonymous_variant 0.25 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625807 c.-897C>A upstream_gene_variant 0.25 bedaquiline
rifampicin
mtrB 3625819 p.Glu265Val missense_variant 0.22 bedaquiline
rifampicin Uncertain significance
lpqB 3625822 c.-912C>T upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3626467 c.147G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
rpoA 3877704 c.804G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878160 c.348C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3878169 c.339G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4038881 c.1824C>A synonymous_variant 0.21 pyrazinamide
clpC1 4038884 c.1821C>T synonymous_variant 0.21 pyrazinamide
clpC1 4038890 c.1815G>A synonymous_variant 0.18 pyrazinamide
clpC1 4039190 c.1515C>T synonymous_variant 0.19 pyrazinamide
clpC1 4039196 c.1509G>A synonymous_variant 0.18 pyrazinamide
clpC1 4039199 p.Ala502Glu missense_variant 0.17 pyrazinamide
clpC1 4039208 c.1497C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.22 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.19 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.88 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
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 4338603 c.-82C>T 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 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R