TB-Profiler result

Run: ERR2229360
Summary

Run ID: ERR2229360

Sample name:

Date: 31-03-2023 17:06:12

Number of reads: 954253

Percentage reads mapped: 98.83

Strain: lineage4.8

Drug-resistance: Other

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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
embR 1417191 p.Asp53His 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
fgd1 490994 p.Gly71Asp missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.5
rpoB 759757 c.-50G>A upstream_gene_variant 0.12
rpoB 760425 p.Glu207* stop_gained 0.13
rpoC 765376 c.2007C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775736 c.2745C>G synonymous_variant 0.13
mmpL5 775741 c.2740C>T synonymous_variant 0.12
mmpL5 776018 c.2463G>C synonymous_variant 0.2
mmpL5 776021 c.2460G>C synonymous_variant 0.18
mmpL5 776837 c.1644T>C synonymous_variant 0.15
mmpL5 777157 c.1324C>A synonymous_variant 0.2
mmpL5 777164 c.1317C>T synonymous_variant 0.2
mmpL5 779244 c.-764G>A upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303150 p.Gly74Ser missense_variant 0.12
fbiC 1303494 p.Leu188Phe missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406619 p.Pro241Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.13
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
fabG1 1673782 p.Gly115Arg missense_variant 0.12
inhA 1674203 c.2T>C start_lost 0.17
inhA 1674969 p.Asp256Glu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103062 c.-20C>A upstream_gene_variant 0.2
katG 2154805 p.Leu436Arg missense_variant 0.22
katG 2155732 p.Gln127Arg missense_variant 0.14
PPE35 2167814 c.2799C>T synonymous_variant 0.31
PPE35 2168117 p.Ser832Arg missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169083 c.1530G>A synonymous_variant 0.12
PPE35 2169161 c.1452G>C synonymous_variant 0.12
PPE35 2169278 c.1335T>C synonymous_variant 0.13
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.29
PPE35 2169293 c.1320T>C synonymous_variant 0.17
PPE35 2169754 p.Phe287Ile missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.76
PPE35 2170053 p.Thr187Ser missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289471 c.-230C>T upstream_gene_variant 0.13
pncA 2289786 c.-545G>T upstream_gene_variant 0.25
folC 2747494 p.Asp35Glu missense_variant 0.13
pepQ 2859407 p.Ile338Val missense_variant 0.12
pepQ 2860453 c.-35A>T upstream_gene_variant 0.13
ribD 2987039 p.Asp67Glu missense_variant 0.12
Rv2752c 3066045 p.Phe49Leu missense_variant 0.18
Rv2752c 3066225 c.-34G>T upstream_gene_variant 0.22
thyX 3067224 p.Val241Gly missense_variant 0.11
thyX 3067621 p.Val109Leu missense_variant 0.13
thyA 3073817 c.654_655insA frameshift_variant 0.13
fbiD 3339734 p.Ala206Gly missense_variant 0.22
fprA 3474278 p.Gly91Val missense_variant 0.15
Rv3236c 3612306 p.Ala271Ser missense_variant 0.12
fbiB 3642325 p.Arg264Leu missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3877934 c.574C>T synonymous_variant 0.12
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4038752 p.Gln651His missense_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.22
embC 4240801 c.939C>T synonymous_variant 0.13
embC 4240803 p.Tyr314Phe missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.27
embB 4246555 c.42G>C synonymous_variant 0.35
embB 4246556 p.Ala15Pro missense_variant 0.35
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4248053 p.Pro514Thr missense_variant 0.18
ubiA 4269139 p.Cys232Phe missense_variant 0.24
ethR 4327348 c.-201G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407597 c.606G>A synonymous_variant 0.17
gid 4407819 c.384G>A synonymous_variant 0.2
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0