TB-Profiler result

Run: ERR2229500

Summary

Run ID: ERR2229500

Sample name:

Date: 31-03-2023 17:16:23

Number of reads: 822340

Percentage reads mapped: 99.07

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 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
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
mshA 576108 p.Ala254Gly missense_variant 0.23
rpoC 766960 c.3591C>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775927 c.2554C>T synonymous_variant 0.15
mmpL5 775931 c.2550C>T synonymous_variant 0.17
mmpL5 776018 c.2463G>C synonymous_variant 0.25
mmpL5 776021 c.2460G>C synonymous_variant 0.25
mmpL5 776419 p.Ser688Pro missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781644 p.Gln29Lys missense_variant 0.18
fbiC 1303012 c.85delG frameshift_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305094 p.His722Asn missense_variant 0.12
Rv1258c 1406388 p.Cys318Phe missense_variant 0.22
Rv1258c 1407235 c.104_105delTG frameshift_variant 0.12
embR 1416485 p.Ala288Val missense_variant 0.12
embR 1416963 p.Gly129Ser missense_variant 0.25
embR 1417226 c.121delA frameshift_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473182 n.1337T>A non_coding_transcript_exon_variant 0.22
rrl 1473443 n.-215T>C upstream_gene_variant 0.12
rrl 1473455 n.-202delC upstream_gene_variant 0.12
rrl 1473694 n.37C>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918142 p.His68Arg missense_variant 0.12
PPE35 2167718 p.Ser965Arg missense_variant 0.18
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169029 p.Asp528Glu missense_variant 0.22
PPE35 2169053 c.1560T>G synonymous_variant 0.22
PPE35 2169269 c.1344A>G synonymous_variant 0.3
PPE35 2169272 c.1341C>G synonymous_variant 0.31
PPE35 2169278 c.1335T>C synonymous_variant 0.27
PPE35 2169281 c.1332T>G synonymous_variant 0.27
PPE35 2169287 c.1326T>C synonymous_variant 0.23
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.51
PPE35 2170202 c.411A>G synonymous_variant 0.12
Rv1979c 2222976 c.189C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289324 c.-83C>A upstream_gene_variant 0.22
pncA 2289429 c.-188G>T upstream_gene_variant 0.22
kasA 2518367 p.Arg85Trp missense_variant 0.12
kasA 2518606 c.492G>C synonymous_variant 0.21
kasA 2518609 p.Met165Ile missense_variant 0.24
folC 2747731 c.-133C>T upstream_gene_variant 0.5
pepQ 2859416 p.Gly335Ser missense_variant 0.15
thyX 3067340 c.606G>A synonymous_variant 0.25
thyX 3067484 p.Phe154Leu missense_variant 0.18
thyX 3067490 c.456C>A synonymous_variant 0.18
thyX 3067942 p.Ala2Pro missense_variant 0.18
thyA 3074571 c.-100T>C upstream_gene_variant 0.36
thyA 3074579 c.-108G>A upstream_gene_variant 0.22
thyA 3074580 c.-109T>C upstream_gene_variant 0.25
ald 3087319 p.Glu167Gly missense_variant 0.25
ald 3087379 p.Ala187Asp missense_variant 0.22
fprA 3474567 c.561C>A synonymous_variant 0.14
whiB7 3568703 c.-24A>T upstream_gene_variant 0.12
Rv3236c 3612879 p.Thr80Ser missense_variant 0.33
alr 3840775 p.Thr216Ala missense_variant 0.11
alr 3841079 p.His114Gln missense_variant 0.14
alr 3841085 c.332_335delCCTG frameshift_variant 0.14
alr 3841171 p.Ala84Ser missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.23
rpoA 3878166 c.342C>A synonymous_variant 0.2
rpoA 3878344 p.Arg55Pro missense_variant 0.17
clpC1 4039018 p.Ser563Ala missense_variant 0.12
clpC1 4039022 c.1683A>G synonymous_variant 0.13
clpC1 4039031 c.1674T>C synonymous_variant 0.12
embC 4240935 p.Val358Ala missense_variant 0.12
embC 4241657 p.Ser599Ala missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243787 c.555G>T synonymous_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.36
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.44
embB 4246556 p.Ala15Pro missense_variant 0.44
embB 4246563 p.Leu17Trp missense_variant 0.56
embB 4246567 c.54G>T synonymous_variant 0.56
embB 4246747 p.Asp78Glu missense_variant 0.18
embB 4247072 p.Gly187Trp missense_variant 0.22
embB 4247512 c.999T>C synonymous_variant 0.14
embB 4247516 p.Asn335Asp missense_variant 0.14
embB 4247826 p.Ala438Gly missense_variant 0.29
embB 4249071 p.Gln853Arg missense_variant 0.12
embB 4249777 c.3264G>T synonymous_variant 0.12
aftB 4267003 p.Arg612Trp missense_variant 0.15
ubiA 4269057 p.Ile259Met missense_variant 0.17
ubiA 4269288 p.Phe182Leu missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0