TB-Profiler result

Run: ERR2229161
Summary

Run ID: ERR2229161

Sample name:

Date: 31-03-2023 16:46:05

Number of reads: 635553

Percentage reads mapped: 99.15

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 2155611 c.500delT frameshift_variant 0.12 isoniazid
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 5805 p.Thr189Asn missense_variant 0.11
gyrA 6652 c.-650C>A upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7947 c.646C>T synonymous_variant 0.15
mshA 575178 c.-170C>A upstream_gene_variant 0.22
mshA 575251 c.-97G>T upstream_gene_variant 0.2
rpoB 761292 p.Val496Leu missense_variant 0.18
rpoB 761666 c.1860G>A synonymous_variant 0.18
rpoB 762331 p.Ile842Asn missense_variant 0.18
rpoC 762848 c.-522G>A upstream_gene_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 0.22
rpoC 764375 p.Ala336Thr missense_variant 0.18
rpoC 766024 c.2655C>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.22
mmpL5 776021 c.2460G>C synonymous_variant 0.22
mmpL5 777174 p.Arg436Leu missense_variant 0.15
mmpL5 777191 c.1290C>A synonymous_variant 0.15
mmpL5 777196 p.Glu429Gln missense_variant 0.18
mmpL5 777881 c.600C>G synonymous_variant 0.12
mmpL5 779175 c.-695G>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801100 p.Gly98Trp missense_variant 0.15
fbiC 1303176 p.Leu82Phe missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303771 p.His281Asn missense_variant 0.14
Rv1258c 1406744 c.597G>A synonymous_variant 0.13
Rv1258c 1407032 c.309G>T synonymous_variant 0.25
Rv1258c 1407164 c.177G>A synonymous_variant 0.33
Rv1258c 1407235 c.104_105delTG frameshift_variant 0.25
Rv1258c 1407243 p.Leu33Gln missense_variant 0.25
embR 1417234 c.114G>A synonymous_variant 0.15
atpE 1461142 c.99delC frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472417 n.572G>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474030 n.373G>T non_coding_transcript_exon_variant 0.22
rrl 1476072 n.2415T>A non_coding_transcript_exon_variant 0.22
rrl 1476551 n.2894T>A non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
rpsA 1833914 p.Ala125Ser missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101910 p.Ala378Val missense_variant 0.17
ndh 2103063 c.-21C>T upstream_gene_variant 0.18
ndh 2103223 c.-181C>A upstream_gene_variant 0.29
katG 2153933 p.Ala727Pro missense_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169029 p.Asp528Glu missense_variant 0.2
PPE35 2169457 p.His386Asp missense_variant 0.14
PPE35 2169890 c.723C>T synonymous_variant 0.16
PPE35 2169893 c.720C>A synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.56
PPE35 2170053 p.Thr187Ser missense_variant 0.62
PPE35 2170238 c.375T>G synonymous_variant 0.13
PPE35 2170247 p.Ile122Met missense_variant 0.13
PPE35 2170371 p.Thr81Val missense_variant 0.4
PPE35 2170561 c.51delC frameshift_variant 0.2
PPE35 2170568 p.Ile15Met missense_variant 0.18
PPE35 2170573 c.40T>C synonymous_variant 0.17
PPE35 2170574 c.39C>G synonymous_variant 0.17
Rv1979c 2222175 p.Leu330Phe missense_variant 0.17
Rv1979c 2223000 c.165C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289667 c.-426C>A upstream_gene_variant 0.18
kasA 2518223 p.Leu37Met missense_variant 0.12
kasA 2518288 c.174C>T synonymous_variant 0.15
kasA 2518606 c.492G>C synonymous_variant 0.26
kasA 2518609 p.Met165Ile missense_variant 0.29
kasA 2519140 c.1026G>C synonymous_variant 0.33
kasA 2519143 c.1029G>C synonymous_variant 0.33
ahpC 2725978 c.-215G>T upstream_gene_variant 0.25
pepQ 2859416 p.Gly335Cys missense_variant 0.13
pepQ 2859762 p.Lys219Asn missense_variant 0.22
pepQ 2860561 c.-143C>A upstream_gene_variant 0.18
ribD 2986657 c.-182C>A upstream_gene_variant 0.22
ribD 2986875 p.Pro13Thr missense_variant 0.14
Rv2752c 3064835 p.Ile453Phe missense_variant 0.12
thyA 3074648 c.-177T>A upstream_gene_variant 0.18
ald 3087459 p.Arg214Trp missense_variant 0.33
fbiD 3339642 c.525T>C synonymous_variant 0.18
fprA 3474529 p.Arg175Cys missense_variant 0.22
fprA 3475297 p.Arg431Gly missense_variant 0.25
Rv3236c 3613110 p.Val3Phe missense_variant 0.12
fbiA 3640482 c.-61T>C upstream_gene_variant 0.15
alr 3840555 p.Ala289Val missense_variant 0.12
rpoA 3878203 p.Pro102Gln missense_variant 0.17
ddn 3986876 c.33G>T synonymous_variant 0.13
clpC1 4038353 p.Gln784His missense_variant 0.14
clpC1 4039003 p.Asn568Asp missense_variant 0.12
clpC1 4039373 p.Phe444Leu missense_variant 0.2
clpC1 4039602 p.Ala368Val missense_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.13
clpC1 4040325 p.Leu127Pro missense_variant 0.17
clpC1 4040411 c.294T>G synonymous_variant 0.18
clpC1 4040415 p.Gln97Arg missense_variant 0.2
clpC1 4040417 c.288G>T synonymous_variant 0.2
embC 4239827 c.-36C>T upstream_gene_variant 0.13
embC 4240789 c.927T>C synonymous_variant 0.11
embC 4241528 p.Arg556Cys missense_variant 0.25
embC 4242165 p.Pro768Leu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243889 c.657G>A synonymous_variant 0.2
embB 4248649 c.2136T>G synonymous_variant 0.2
embB 4249364 p.Glu951Lys missense_variant 0.14
aftB 4267034 c.1803C>G synonymous_variant 0.12
aftB 4268043 p.Ala265Glu missense_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.17
ethR 4326964 c.-585G>A upstream_gene_variant 0.17
ethR 4326970 c.-579G>T upstream_gene_variant 0.15
ethR 4327018 c.-531G>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407797 p.Ser136Thr missense_variant 0.14
gid 4408244 c.-42C>A upstream_gene_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0