TB-Profiler result

Run: ERR2229243
Summary

Run ID: ERR2229243

Sample name:

Date: 31-03-2023 16:51:54

Number of reads: 1100086

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 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 575716 c.369C>T synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.23
ccsA 619968 c.78G>A synonymous_variant 0.33
rpoB 760780 p.Ser325Leu missense_variant 0.2
rpoB 761128 p.Ser441* stop_gained 0.15
rpoB 761358 p.Val518Ile missense_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 775747 p.Met912Leu missense_variant 0.15
mmpL5 775748 c.2733T>C synonymous_variant 0.15
mmpL5 775903 p.Glu860* stop_gained 0.15
mmpL5 777311 c.1170C>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304814 p.Met628Ile missense_variant 0.14
embR 1416881 p.Phe156Ser missense_variant 0.17
atpE 1460849 c.-196G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
fabG1 1673560 p.Lys41Gln missense_variant 0.12
fabG1 1673872 c.436_437delGG frameshift_variant 0.22
fabG1 1674058 p.Pro207Thr missense_variant 0.2
rpsA 1834839 p.Glu433Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918521 c.582C>A synonymous_variant 0.14
PPE35 2167814 c.2799C>T synonymous_variant 0.18
PPE35 2168059 p.Gln852Lys missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.22
PPE35 2169281 c.1332T>G synonymous_variant 0.21
PPE35 2169287 c.1326T>C synonymous_variant 0.15
PPE35 2169457 p.His386Asp missense_variant 0.12
PPE35 2169602 c.1011C>A synonymous_variant 0.17
PPE35 2169902 c.711G>C synonymous_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.23
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.39
PPE35 2170189 p.Glu142Gln missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519057 p.Thr315Ser missense_variant 0.15
kasA 2519062 c.948T>G synonymous_variant 0.12
kasA 2519066 c.956_982delACGCCGCGGAGGCCAACGCCATCCGCG disruptive_inframe_deletion 0.2
kasA 2519143 c.1029G>C synonymous_variant 0.12
folC 2746155 p.Phe482Ile missense_variant 0.12
Rv2752c 3067017 c.-826G>T upstream_gene_variant 0.12
thyA 3074228 p.Glu82Lys missense_variant 0.18
fprA 3474165 c.159C>G synonymous_variant 0.18
fprA 3474707 p.Thr234Asn missense_variant 0.12
fprA 3475325 p.Pro440Arg missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.24
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039829 p.Leu292Phe missense_variant 0.15
clpC1 4040072 c.633C>T synonymous_variant 0.17
panD 4044060 c.222C>A synonymous_variant 0.2
panD 4044096 c.186C>G synonymous_variant 0.19
embC 4241532 p.Ile557Thr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244683 p.Arg484Pro missense_variant 0.15
embB 4248677 p.Met722Leu missense_variant 0.12
aftB 4267792 p.Pro349Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408338 c.-136A>C upstream_gene_variant 0.2
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0