TB-Profiler result

Run: ERR2245345
Summary

Run ID: ERR2245345

Sample name:

Date: 31-03-2023 17:38:59

Number of reads: 2210111

Percentage reads mapped: 98.41

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.99
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 1918629 c.692delC frameshift_variant 0.11 capreomycin
katG 2155999 p.Trp38* stop_gained 0.2 isoniazid
ethA 4327347 p.Gly43Ser missense_variant 0.18 ethionamide
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 6178 c.939C>T synonymous_variant 0.22
gyrA 7234 c.-68C>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7666 p.Asp122Ala missense_variant 0.29
gyrA 7746 p.Thr149Ser missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490820 p.Glu13Gly missense_variant 0.17
fgd1 491315 p.Gly178Ala missense_variant 0.29
fgd1 491491 p.Pro237Ser missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575725 c.378C>A synonymous_variant 0.12
mshA 576278 p.Gly311* stop_gained 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762502 p.Pro899Leu missense_variant 1.0
rpoB 762844 p.Phe1013Ser missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763952 p.Arg195Ser missense_variant 0.14
rpoC 764048 p.Thr227Ser missense_variant 0.25
rpoC 764301 p.Gly311Val missense_variant 0.4
rpoC 764402 p.Arg345Ser missense_variant 0.25
rpoC 765162 p.Glu598Gly missense_variant 0.14
rpoC 766004 p.Asp879Tyr missense_variant 0.15
rpoC 767113 c.3744G>C synonymous_variant 0.11
rpoC 767267 p.Ala1300Thr missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776840 c.1641C>T synonymous_variant 0.13
mmpL5 777044 c.1437C>G synonymous_variant 0.29
mmpL5 777128 c.1353A>G synonymous_variant 0.15
mmpL5 777214 p.Ala423Thr missense_variant 0.14
mmpL5 777737 c.744T>G synonymous_variant 0.3
mmpL5 778078 p.Thr135Pro missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781445 c.-115G>T upstream_gene_variant 0.2
rplC 800894 p.Val29Gly missense_variant 0.2
rplC 800924 p.Ile39Thr missense_variant 0.12
fbiC 1302802 c.-129G>C upstream_gene_variant 0.18
fbiC 1303411 p.Trp161Arg missense_variant 0.12
fbiC 1303723 p.Glu265* stop_gained 0.29
fbiC 1305106 c.2176C>T synonymous_variant 0.22
embR 1416432 p.Ala306Ser missense_variant 0.13
embR 1416999 p.Ala117Thr missense_variant 0.18
embR 1417453 c.-106G>A upstream_gene_variant 0.2
atpE 1461078 p.Gly12Ser missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476160 n.2507delA non_coding_transcript_exon_variant 1.0
inhA 1674569 p.Ser123* stop_gained 0.22
rpsA 1834443 p.Val301Gly missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102030 p.Gln338Pro missense_variant 0.2
ndh 2102861 p.Gly61Val missense_variant 0.5
ndh 2102941 p.Lys34Asn missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154877 p.Trp412Leu missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169053 c.1560T>A synonymous_variant 0.22
PPE35 2169063 p.Met517Lys missense_variant 0.25
PPE35 2169269 c.1344A>G synonymous_variant 0.18
PPE35 2169272 c.1341C>G synonymous_variant 0.18
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169287 c.1326T>C synonymous_variant 0.18
PPE35 2169293 c.1320T>C synonymous_variant 0.2
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2222254 p.Ile304Asn missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289251 c.-10T>A upstream_gene_variant 0.14
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289716 c.-475T>C upstream_gene_variant 0.25
kasA 2517962 c.-153C>T upstream_gene_variant 0.22
kasA 2519139 p.Ala342Val missense_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747457 p.Thr48Pro missense_variant 0.22
pepQ 2860607 c.-189A>C upstream_gene_variant 0.4
thyX 3067776 p.Asn57Thr missense_variant 0.43
thyX 3067799 p.Lys49Asn missense_variant 0.25
thyA 3074318 p.Phe52Ile missense_variant 0.29
thyA 3074421 c.51C>A synonymous_variant 0.29
thyA 3074642 c.-171T>C upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087180 p.Gln121Lys missense_variant 0.17
ald 3087284 c.465C>A synonymous_variant 0.13
Rv3083 3449546 p.Leu348Pro missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568461 c.219A>G synonymous_variant 0.11
whiB7 3568557 c.123A>T synonymous_variant 0.15
Rv3236c 3612184 p.Phe311Leu missense_variant 0.2
Rv3236c 3612239 p.Val293Ala missense_variant 0.15
fbiA 3641156 p.Asp205Ala missense_variant 0.29
fbiB 3641745 p.Asp71His missense_variant 0.2
fbiB 3641890 p.Ala119Val missense_variant 0.17
fbiB 3642182 c.648G>A synonymous_variant 0.12
fbiB 3642534 p.Arg334Trp missense_variant 0.22
fbiB 3642648 p.Met372Val missense_variant 0.29
rpoA 3877926 c.582G>T synonymous_variant 0.25
rpoA 3878490 c.18C>G synonymous_variant 0.57
ddn 3986753 c.-91G>T upstream_gene_variant 0.15
ddn 3986754 c.-90T>G upstream_gene_variant 0.23
embC 4239879 p.Ala6Gly missense_variant 0.31
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240696 c.834C>A synonymous_variant 0.29
embC 4241182 c.1320G>T synonymous_variant 0.2
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241648 p.Leu596Val missense_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242842 p.Gln994* stop_gained 0.18
embA 4245401 c.2169G>T synonymous_variant 0.14
embA 4245495 p.Gly755Cys missense_variant 0.14
embA 4245509 c.2277A>T synonymous_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246657 c.144C>G synonymous_variant 0.2
aftB 4267625 c.1212T>C synonymous_variant 0.12
aftB 4268014 p.Pro275Ser missense_variant 0.15
aftB 4268468 c.369G>A synonymous_variant 0.17
aftB 4269504 c.-668A>T upstream_gene_variant 0.21
ethA 4326039 p.Arg479Gly missense_variant 0.13
ethA 4326418 c.1056G>A synonymous_variant 0.18
ethA 4327161 p.Ile105Val missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0