TB-Profiler result

Run: ERR2229070
Summary

Run ID: ERR2229070

Sample name:

Date: 31-03-2023 16:35:19

Number of reads: 840620

Percentage reads mapped: 99.33

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
gyrB 7202 p.Asp655Tyr missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9147 p.Gly616Ser missense_variant 0.13
mshA 575832 p.Gly162Val missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576223 c.876G>A synonymous_variant 0.15
ccsA 620455 p.Ala189Thr missense_variant 0.12
rpoB 761012 c.1206C>T synonymous_variant 0.12
rpoB 762967 p.Lys1054Arg missense_variant 0.1
rpoC 764323 c.954G>A synonymous_variant 0.17
rpoC 764857 c.1488G>T synonymous_variant 0.13
rpoC 765009 p.Leu547Trp missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776007 p.His825Leu missense_variant 0.2
mmpL5 778768 c.-288T>C upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304041 p.Trp371Arg missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473038 n.1193A>G non_coding_transcript_exon_variant 0.12
rrl 1473407 n.-251A>C upstream_gene_variant 0.12
rrl 1473409 n.-249T>A upstream_gene_variant 0.12
rrl 1473411 n.-247G>T upstream_gene_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.1
fabG1 1673361 c.-79C>G upstream_gene_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
fabG1 1674076 c.642delC frameshift_variant 0.12
rpsA 1834013 p.Val158Leu missense_variant 0.14
rpsA 1834866 p.Gly442Glu missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.56
PPE35 2170053 p.Thr187Ser missense_variant 0.52
PPE35 2170385 c.228G>T synonymous_variant 0.11
PPE35 2170392 p.Gly74Ala missense_variant 0.11
Rv1979c 2223211 c.-47G>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289666 c.-425C>A upstream_gene_variant 0.22
eis 2714331 c.1002T>C synonymous_variant 0.14
pepQ 2859487 p.Thr311Ile missense_variant 0.11
thyX 3067195 c.751T>A stop_lost&splice_region_variant 0.13
thyX 3067340 c.606G>A synonymous_variant 0.18
thyX 3067890 p.Ala19Asp missense_variant 0.17
ald 3087836 c.1017A>G synonymous_variant 0.22
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474851 p.Arg282His missense_variant 0.18
fbiA 3640880 p.Leu113Arg missense_variant 0.11
fbiB 3642372 p.Val280Phe missense_variant 0.17
embC 4241882 c.2020C>T synonymous_variant 0.18
embC 4242118 c.2256C>G synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244073 c.844delC frameshift_variant 0.15
embB 4246008 c.-506C>A upstream_gene_variant 0.18
embB 4246181 c.-333C>A upstream_gene_variant 0.13
embA 4246281 p.Ser1017Pro missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.36
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246641 p.Ala43Glu missense_variant 0.13
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4248628 c.2115C>T synonymous_variant 0.25
embB 4249363 c.2850C>G synonymous_variant 0.12
embB 4249364 p.Glu951Lys missense_variant 0.12
ubiA 4269227 p.Gly203Cys missense_variant 0.29
ethA 4326618 p.Tyr286His missense_variant 0.11
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0