TB-Profiler result

Run: ERR2229483
Summary

Run ID: ERR2229483

Sample name:

Date: 31-03-2023 17:15:27

Number of reads: 972630

Percentage reads mapped: 99.13

Strain: lineage4.8

Drug-resistance: Sensitive

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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 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
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 7194 p.Met652Arg missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575831 p.Gly162Cys missense_variant 0.22
rpoB 759759 c.-47_-46delCC upstream_gene_variant 0.12
rpoB 760930 p.Val375Ala missense_variant 0.17
rpoB 760956 p.Arg384Gly missense_variant 0.17
rpoB 763095 p.Tyr1097His missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776511 p.Ser657Phe missense_variant 0.13
mmpL5 776807 c.1674G>T synonymous_variant 0.22
mmpL5 776894 c.1587T>C synonymous_variant 0.11
mmpL5 777191 c.1290C>A synonymous_variant 0.12
mmpL5 777196 p.Glu429Gln missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304309 p.Thr460Ile missense_variant 0.15
fbiC 1305076 p.Pro716Thr missense_variant 0.15
Rv1258c 1406224 p.Ala373Pro missense_variant 0.11
Rv1258c 1406944 p.Ala133Thr missense_variant 0.2
embR 1416861 p.Ala163Pro missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473097 n.1252G>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475169 n.1512G>T non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167997 c.2616G>C synonymous_variant 0.2
PPE35 2168222 c.2391G>T synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.2
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169287 c.1326T>C synonymous_variant 0.21
PPE35 2169293 c.1320T>C synonymous_variant 0.21
PPE35 2169457 p.His386Asp missense_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170147 p.Ser156Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289752 c.-511G>A upstream_gene_variant 0.13
pncA 2290057 c.-816G>T upstream_gene_variant 0.13
kasA 2518889 p.Ala259Ser missense_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.2
kasA 2519143 c.1029G>C synonymous_variant 0.2
eis 2714705 p.Gly210* stop_gained 0.17
ribD 2987196 p.Val120Leu missense_variant 0.15
Rv3083 3448385 c.-119C>T upstream_gene_variant 0.15
fprA 3474274 p.Pro90Ser missense_variant 0.15
Rv3236c 3612006 p.Arg371Cys missense_variant 0.12
clpC1 4039787 c.918G>T synonymous_variant 0.14
clpC1 4039829 p.Leu292Ile missense_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.17
clpC1 4040447 c.257delA frameshift_variant 0.18
embC 4241153 p.Ile431Phe missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.15
embA 4244044 p.Ser271* stop_gained 0.12
embA 4245901 p.Gln890Arg missense_variant 0.13
embA 4246074 p.Leu948Met missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.16
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246747 p.Asp78Glu missense_variant 0.2
embB 4247470 c.957T>C synonymous_variant 0.12
embB 4247988 p.Val492Ala missense_variant 0.15
aftB 4268766 p.Arg24Leu missense_variant 0.2
ethR 4327303 c.-246G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407843 p.Glu120Asp missense_variant 0.11
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0