TB-Profiler result

Run: ERR1950004
Summary

Run ID: ERR1950004

Sample name:

Date: 31-03-2023 15:37:13

Number of reads: 631246

Percentage reads mapped: 99.32

Strain: lineage4

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
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
katG 2155405 p.Asn236Thr missense_variant 0.29 isoniazid
embB 4247401 p.Asn296Lys missense_variant 0.31 ethambutol
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
gyrB 5724 p.Ala162Glu missense_variant 0.18
gyrB 6071 p.Phe278Ile missense_variant 0.29
gyrB 6542 p.Ile435Phe missense_variant 0.67
gyrB 7259 p.Asp674Tyr missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8074 p.Glu258Val missense_variant 0.18
gyrA 9161 c.1860C>G synonymous_variant 0.18
fgd1 491167 p.Phe129Val missense_variant 0.23
fgd1 491489 p.Asp236Ala missense_variant 0.29
fgd1 491683 p.Val301Leu missense_variant 0.22
ccsA 619772 c.-119A>C upstream_gene_variant 0.18
ccsA 619787 c.-104T>G upstream_gene_variant 0.36
ccsA 619964 p.Leu25Arg missense_variant 0.22
ccsA 619985 p.Leu32Pro missense_variant 0.18
ccsA 620262 c.372C>T synonymous_variant 0.18
rpoB 760024 p.Asp73Gly missense_variant 0.12
rpoB 763257 p.Arg1151Trp missense_variant 0.18
rpoC 763992 p.Ile208Ser missense_variant 0.29
rpoC 764216 p.Asn283Asp missense_variant 0.22
rpoC 764229 p.Gln287Leu missense_variant 0.38
rpoC 764541 p.Val391Gly missense_variant 0.22
rpoC 767027 p.Trp1220Arg missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776696 c.1785G>T synonymous_variant 0.33
mmpL5 776798 c.1683G>T synonymous_variant 0.5
mmpL5 778341 p.Asn47Thr missense_variant 0.12
mmpS5 778566 p.Cys114Ser missense_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781873 p.Gln105Leu missense_variant 0.27
rplC 800985 c.177A>C synonymous_variant 0.18
fbiC 1302795 c.-136A>C upstream_gene_variant 0.29
fbiC 1303567 p.Met213Leu missense_variant 0.27
fbiC 1303607 p.Lys226Thr missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303982 p.Val351Gly missense_variant 0.25
Rv1258c 1406226 p.Asp372Gly missense_variant 0.29
Rv1258c 1406378 c.963C>A synonymous_variant 0.67
Rv1258c 1406723 p.Gln206His missense_variant 0.17
embR 1416467 p.Asp294Gly missense_variant 0.18
embR 1416518 p.Leu277Arg missense_variant 0.29
embR 1417028 p.Asp107Ala missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471745 n.-101T>A upstream_gene_variant 0.25
rrs 1471764 n.-82C>A upstream_gene_variant 0.2
rrs 1472270 n.425T>G non_coding_transcript_exon_variant 0.22
rrs 1473212 n.1367A>G non_coding_transcript_exon_variant 0.15
rrl 1473881 n.224A>T non_coding_transcript_exon_variant 0.2
rrl 1473882 n.225A>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474515 n.858G>T non_coding_transcript_exon_variant 0.17
rrl 1475353 n.1696A>G non_coding_transcript_exon_variant 0.15
rrl 1475570 n.1913A>T non_coding_transcript_exon_variant 0.29
rrl 1475674 n.2017A>T non_coding_transcript_exon_variant 0.5
rrl 1476779 n.3122G>T non_coding_transcript_exon_variant 0.22
inhA 1674936 c.735G>T synonymous_variant 0.29
rpsA 1833502 c.-40T>A upstream_gene_variant 0.24
rpsA 1834857 p.Glu439Gly missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918429 p.Leu164Val missense_variant 0.38
ndh 2102108 p.Pro312Arg missense_variant 0.17
katG 2154410 p.Thr568Pro missense_variant 0.23
katG 2155140 c.972C>A synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.4
PPE35 2169023 c.1590G>T synonymous_variant 0.5
PPE35 2170216 p.Ile133Leu missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289114 p.His43Arg missense_variant 0.17
pncA 2289123 p.Asp40Gly missense_variant 0.15
pncA 2289464 c.-223A>G upstream_gene_variant 0.2
kasA 2518627 p.Cys171Trp missense_variant 0.25
eis 2715469 c.-137T>A upstream_gene_variant 0.33
ahpC 2726218 p.Gln9Arg missense_variant 0.18
ahpC 2726348 p.Phe52Leu missense_variant 0.21
folC 2746170 p.Ala477Ser missense_variant 0.33
folC 2746491 p.Phe370Ile missense_variant 0.2
folC 2746823 p.Glu259Val missense_variant 0.4
folC 2747070 p.Met177Val missense_variant 0.25
folC 2747605 c.-7C>A upstream_gene_variant 0.22
folC 2747629 c.-31A>C upstream_gene_variant 0.18
folC 2747729 c.-131A>C upstream_gene_variant 0.25
pepQ 2859956 p.Thr155Pro missense_variant 0.2
ribD 2987043 p.Phe69Ile missense_variant 0.2
Rv2752c 3064566 c.1626G>C synonymous_variant 0.33
Rv2752c 3064759 p.Val478Glu missense_variant 0.29
Rv2752c 3064906 p.Val429Gly missense_variant 0.33
Rv2752c 3066070 p.Leu41* stop_gained 0.2
thyX 3067277 c.669C>G synonymous_variant 0.2
thyX 3067304 p.Glu214Asp missense_variant 0.25
Rv3083 3448448 c.-56A>T upstream_gene_variant 0.5
fprA 3474067 p.Ser21Ala missense_variant 0.18
fprA 3474138 c.132T>A synonymous_variant 0.25
fprA 3475211 p.His402Pro missense_variant 0.18
Rv3236c 3612984 p.Asn45Tyr missense_variant 0.4
Rv3236c 3613146 c.-30T>G upstream_gene_variant 0.31
fbiA 3641195 p.Val218Asp missense_variant 0.22
fbiB 3641798 c.264C>T synonymous_variant 0.14
fbiB 3642355 p.Asp274Ala missense_variant 0.17
fbiB 3642751 p.Asp406Ala missense_variant 0.22
alr 3841559 c.-139C>T upstream_gene_variant 0.5
alr 3841612 c.-192A>C upstream_gene_variant 0.25
rpoA 3877523 p.Thr329Ala missense_variant 0.17
rpoA 3878159 p.Thr117Pro missense_variant 0.2
rpoA 3878269 p.Leu80Pro missense_variant 0.18
rpoA 3878490 c.18C>G synonymous_variant 0.4
clpC1 4038573 p.Asn711Thr missense_variant 0.29
clpC1 4038706 p.Asn667Tyr missense_variant 0.29
clpC1 4038966 p.Ile580Asn missense_variant 0.29
panD 4043998 p.Asp95Ala missense_variant 0.17
embC 4240982 p.Ser374Arg missense_variant 0.4
embC 4242354 p.Gly831Val missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 0.93
embA 4243433 c.201A>C synonymous_variant 0.18
embA 4245431 p.Cys733Trp missense_variant 0.17
embA 4245633 p.Lys801Glu missense_variant 0.22
embA 4245640 p.Asn803Thr missense_variant 0.22
embA 4245706 p.His825Pro missense_variant 0.31
embB 4246736 p.Thr75Pro missense_variant 0.33
embB 4247147 p.Thr212Pro missense_variant 0.33
embB 4247471 p.Phe320Ile missense_variant 0.23
aftB 4267386 p.His484Arg missense_variant 0.2
ubiA 4270021 c.-188T>C upstream_gene_variant 0.13
ethA 4327824 c.-351C>T upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0