TB-Profiler result

Run: ERR2229744
Summary

Run ID: ERR2229744

Sample name:

Date: 31-03-2023 17:33:13

Number of reads: 1193536

Percentage reads mapped: 99.2

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
fgd1 491042 p.Ala87Asp missense_variant 0.14
fgd1 491182 p.Glu134* stop_gained 0.14
rpoB 760409 p.Ser201Arg missense_variant 0.17
rpoB 760590 p.Val262Ile missense_variant 0.11
rpoB 762825 p.Gly1007Arg missense_variant 0.14
rpoC 765060 p.Asn564Ile missense_variant 0.12
rpoC 765682 p.Asn771Lys missense_variant 0.15
rpoC 766975 c.3606C>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776745 p.Arg579His missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304005 p.Pro359Thr missense_variant 0.22
Rv1258c 1406946 p.Ala132Gly missense_variant 0.1
atpE 1461008 c.-37G>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474742 n.1085A>G non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.28
fabG1 1673349 c.-91G>C upstream_gene_variant 0.28
fabG1 1673357 c.-83G>A upstream_gene_variant 0.26
fabG1 1673359 c.-81T>C upstream_gene_variant 0.26
fabG1 1673361 c.-79C>G upstream_gene_variant 0.26
fabG1 1673380 c.-60C>G upstream_gene_variant 0.41
rpsA 1833392 c.-150C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155235 p.Leu293Met missense_variant 0.22
katG 2155998 p.Trp38Cys missense_variant 0.12
PPE35 2167965 c.2646_2647delAG frameshift_variant 0.12
PPE35 2167973 c.2640A>G synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.17
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.19
PPE35 2169281 c.1332T>G synonymous_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.35
PPE35 2170147 p.Ser156Ala missense_variant 0.21
PPE35 2170159 p.Ala152Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747422 c.177G>T synonymous_variant 0.12
pepQ 2859418 p.Gly334Asp missense_variant 0.12
fprA 3474908 p.Arg301Pro missense_variant 0.17
fbiB 3641632 p.Val33Asp missense_variant 0.11
fbiB 3642768 p.Leu412Met missense_variant 0.12
rpoA 3877863 c.645G>T synonymous_variant 0.14
rpoA 3878636 c.-129C>G upstream_gene_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244278 p.Pro349Gln missense_variant 0.12
embA 4244930 c.1698G>C synonymous_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.44
embB 4246548 p.Pro12Gln missense_variant 0.53
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.28
embB 4246567 c.54G>T synonymous_variant 0.28
embB 4246832 p.Lys107* stop_gained 0.17
embB 4247036 p.Gly175Cys missense_variant 0.12
embB 4247090 p.Thr193Ala missense_variant 0.15
embB 4247098 c.585C>G synonymous_variant 0.14
embB 4247903 c.1390C>A synonymous_variant 0.11
aftB 4267786 p.Gly351Trp missense_variant 0.17
aftB 4268522 p.Leu105Phe missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0