TB-Profiler result

Run: ERR9891961
Summary

Run ID: ERR9891961

Sample name:

Date: 02-04-2023 13:25:00

Number of reads: 533539

Percentage reads mapped: 99.42

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
tlyA 1918412 c.474delC frameshift_variant 0.12 capreomycin
katG 2155930 c.180_181delGG frameshift_variant 0.18 isoniazid
embB 4247925 p.Arg471Pro missense_variant 0.11 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8615 p.Met438Ile missense_variant 0.17
fgd1 490724 c.-59G>A upstream_gene_variant 0.18
fgd1 490744 c.-39T>C upstream_gene_variant 0.15
fgd1 490933 p.Ala51Ser missense_variant 0.4
fgd1 491191 p.Gly137Trp missense_variant 0.12
fgd1 491316 c.534C>G synonymous_variant 0.17
fgd1 491481 c.699C>T synonymous_variant 0.12
mshA 575152 c.-196G>T upstream_gene_variant 0.29
rpoB 760477 p.Arg224Leu missense_variant 0.15
rpoB 761673 p.Gly623Trp missense_variant 0.12
rpoB 762165 p.Gly787Cys missense_variant 0.18
rpoC 762548 c.-822C>T upstream_gene_variant 0.13
rpoC 762707 c.-663G>C upstream_gene_variant 0.12
rpoC 763835 p.Ala156Ser missense_variant 0.14
rpoC 764586 p.Leu406Pro missense_variant 0.12
rpoC 764644 c.1275G>C synonymous_variant 0.12
rpoC 765659 p.Ala764Ser missense_variant 0.12
rpoC 766024 c.2655C>A synonymous_variant 0.14
rpoC 766761 p.Gln1131Pro missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 p.Leu919Met missense_variant 0.17
mmpL5 776225 p.Glu752Asp missense_variant 0.12
mmpL5 776237 c.2244C>A synonymous_variant 0.14
mmpL5 777144 p.Glu446Gly missense_variant 0.17
mmpL5 777967 p.Ile172Val missense_variant 0.2
mmpL5 778205 p.Met92Ile missense_variant 0.11
mmpR5 779023 p.Ala12Ser missense_variant 0.18
mmpL5 779298 c.-818G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801084 c.276G>T synonymous_variant 0.13
fbiC 1303966 p.Leu346Met missense_variant 0.2
fbiC 1304114 p.Gln395Arg missense_variant 0.29
fbiC 1305026 p.Glu699Gly missense_variant 0.18
Rv1258c 1406292 p.Gly350Ala missense_variant 0.15
Rv1258c 1406365 p.Gly326* stop_gained 0.18
Rv1258c 1406887 p.Leu152Met missense_variant 0.11
Rv1258c 1407429 c.-90_-89insTGTTCGTGT upstream_gene_variant 0.11
Rv1258c 1407432 c.-92T>G upstream_gene_variant 0.11
embR 1417393 c.-46G>T upstream_gene_variant 0.14
embR 1417403 c.-56G>A upstream_gene_variant 0.15
embR 1417542 c.-195C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673298 c.-142A>C upstream_gene_variant 0.22
fabG1 1673959 p.Ala174Ser missense_variant 0.18
inhA 1673973 c.-229G>T upstream_gene_variant 0.15
fabG1 1674152 p.Pro238Gln missense_variant 0.14
inhA 1674555 p.Lys118Asn missense_variant 0.15
inhA 1674726 c.525G>T synonymous_variant 0.14
inhA 1674856 p.Glu219* stop_gained 0.15
inhA 1674861 p.Glu220Asp missense_variant 0.15
inhA 1674966 c.765T>A synonymous_variant 0.12
rpsA 1833372 c.-170C>A upstream_gene_variant 0.15
tlyA 1917955 p.Arg6Ser missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918008 c.69C>A synonymous_variant 0.5
tlyA 1918225 p.Phe96Ile missense_variant 0.14
ndh 2101793 p.Trp417Leu missense_variant 0.12
ndh 2102514 p.Gly177Trp missense_variant 0.18
ndh 2102743 c.300C>G synonymous_variant 0.11
ndh 2102945 p.Leu33Pro missense_variant 0.12
ndh 2103073 c.-31A>T upstream_gene_variant 0.17
ndh 2103162 c.-120G>T upstream_gene_variant 0.2
katG 2154958 p.Arg385Leu missense_variant 0.22
katG 2155407 c.705G>T synonymous_variant 0.17
PPE35 2170431 p.Ser61* stop_gained 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289270 c.-29G>T upstream_gene_variant 0.2
pncA 2289497 c.-256G>C upstream_gene_variant 0.12
pncA 2289606 c.-365G>T upstream_gene_variant 0.12
pncA 2289743 c.-502A>G upstream_gene_variant 0.12
kasA 2518016 c.-99A>G upstream_gene_variant 0.17
kasA 2518773 p.Asn220Ile missense_variant 0.18
kasA 2518882 c.768C>T synonymous_variant 0.15
eis 2714215 p.Asn373Ser missense_variant 0.14
eis 2714485 p.Arg283Leu missense_variant 0.15
eis 2715023 p.Leu104Met missense_variant 0.29
eis 2715288 c.45G>T synonymous_variant 0.15
folC 2746258 c.1341C>A synonymous_variant 0.2
folC 2746680 p.Ala307Ser missense_variant 0.33
folC 2747447 p.Ser51Ile missense_variant 0.12
folC 2747464 c.135G>T synonymous_variant 0.12
pepQ 2859701 p.Gly240Ser missense_variant 0.14
pepQ 2860037 p.Val128Leu missense_variant 0.14
pepQ 2860381 p.Gln13Arg missense_variant 0.2
pepQ 2860525 c.-107A>T upstream_gene_variant 0.22
ribD 2986655 c.-184A>G upstream_gene_variant 0.11
Rv2752c 3064757 p.Val479Leu missense_variant 0.17
Rv2752c 3065318 p.Ala292Pro missense_variant 0.1
Rv2752c 3065600 p.Leu198Met missense_variant 0.15
Rv2752c 3066338 c.-147G>T upstream_gene_variant 0.22
Rv2752c 3067060 c.-869C>A upstream_gene_variant 0.15
thyX 3067964 c.-19C>T upstream_gene_variant 0.15
thyX 3068154 c.-209G>T upstream_gene_variant 0.11
thyA 3074112 c.360C>A synonymous_variant 0.11
ald 3087195 p.Ala126Ser missense_variant 0.12
ald 3087404 c.585G>T synonymous_variant 0.12
ald 3087542 c.723G>A synonymous_variant 0.12
fprA 3474251 p.Val82Glu missense_variant 0.14
fprA 3474849 p.Lys281Asn missense_variant 0.12
whiB7 3568514 p.Ala56Ser missense_variant 0.4
Rv3236c 3612544 c.573T>C synonymous_variant 0.29
Rv3236c 3612769 c.348T>G synonymous_variant 0.25
Rv3236c 3613077 p.Leu14Met missense_variant 0.13
fbiA 3640810 p.Gln90Lys missense_variant 0.17
fbiA 3640963 p.Arg141Cys missense_variant 0.15
fbiB 3641352 c.-183C>A upstream_gene_variant 0.25
alr 3840489 p.Pro311Gln missense_variant 0.13
alr 3840764 c.657G>C synonymous_variant 1.0
alr 3840935 c.486G>T synonymous_variant 0.15
alr 3841244 c.177G>T synonymous_variant 0.12
rpoA 3877992 c.516C>A synonymous_variant 0.11
ddn 3986851 p.Lys3Arg missense_variant 0.13
ddn 3986863 p.Arg7Pro missense_variant 0.13
clpC1 4038998 p.Phe569Leu missense_variant 0.18
clpC1 4039092 p.Gly538Glu missense_variant 0.25
clpC1 4039761 p.Gly315Asp missense_variant 0.22
clpC1 4040181 p.Gly175Val missense_variant 0.2
clpC1 4040604 p.Leu34Pro missense_variant 0.17
clpC1 4040752 c.-48C>A upstream_gene_variant 0.15
clpC1 4040784 c.-80C>T upstream_gene_variant 0.15
panD 4044312 c.-31G>T upstream_gene_variant 0.12
embC 4240147 c.285C>A synonymous_variant 0.29
embC 4240190 p.Pro110Thr missense_variant 0.29
embC 4242117 p.Ala752Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242900 p.Pro1013Leu missense_variant 0.12
embC 4243112 p.Gly1084Trp missense_variant 0.14
embA 4243243 p.Asp4Val missense_variant 0.15
embA 4243935 p.Asp235Tyr missense_variant 0.22
embA 4246035 p.Glu935* stop_gained 0.18
embA 4246041 p.Asp937Tyr missense_variant 0.18
embB 4246082 c.-432T>C upstream_gene_variant 0.22
embB 4246376 c.-138G>A upstream_gene_variant 0.18
embB 4246946 p.Cys145Gly missense_variant 0.25
embB 4247093 p.Gly194Trp missense_variant 0.14
embB 4247455 c.942C>A synonymous_variant 0.15
embB 4248050 p.Gly513Arg missense_variant 0.11
embB 4249123 c.2610C>T synonymous_variant 0.2
embB 4249230 p.Gly906Glu missense_variant 0.18
embB 4249242 p.Leu910Arg missense_variant 0.15
embB 4249697 p.Gly1062Cys missense_variant 0.15
aftB 4267302 p.Asn512Thr missense_variant 0.18
aftB 4267319 p.Asp506Glu missense_variant 0.22
aftB 4267977 p.Pro287Gln missense_variant 0.14
ethA 4326230 p.Asp415Gly missense_variant 0.12
ethA 4327125 p.Thr117Ala missense_variant 0.11
ethA 4328350 c.-877C>T upstream_gene_variant 0.15
whiB6 4338453 c.69A>G synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338626 c.-105G>T upstream_gene_variant 0.12