TB-Profiler result

Run: ERR2229211
Summary

Run ID: ERR2229211

Sample name:

Date: 31-03-2023 16:48:51

Number of reads: 424320

Percentage reads mapped: 99.66

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
gyrA 8860 p.Ile520Thr missense_variant 0.11
mshA 575491 c.144G>T synonymous_variant 0.18
mshA 576488 p.Val381His missense_variant 0.15
ccsA 619937 p.Trp16Leu missense_variant 0.29
rpoC 764541 p.Val391Gly missense_variant 0.13
rpoC 764543 p.Thr392Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305474 c.2544T>G synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475640 n.1983G>A non_coding_transcript_exon_variant 0.25
rrl 1475904 n.2247G>A non_coding_transcript_exon_variant 0.25
rrl 1476393 n.2736C>A non_coding_transcript_exon_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
fabG1 1673533 p.Ala32Ser missense_variant 0.14
fabG1 1673915 p.Gly159Val missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918411 p.Ile158Val missense_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168819 c.1794T>C synonymous_variant 0.15
PPE35 2169386 c.1227C>A synonymous_variant 0.12
PPE35 2169394 p.Ala407Thr missense_variant 0.12
PPE35 2169488 c.1125G>C synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.4
PPE35 2170298 c.315A>G synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290231 c.-990G>A upstream_gene_variant 0.25
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.15
eis 2714576 p.Trp253Gly missense_variant 0.29
eis 2715432 c.-100C>T upstream_gene_variant 0.12
folC 2747561 p.Ser13* stop_gained 0.29
ribD 2987309 c.471G>A synonymous_variant 0.29
Rv2752c 3064865 p.Pro443Thr missense_variant 0.14
thyA 3074648 c.-177T>G upstream_gene_variant 0.42
Rv3236c 3612115 c.1002G>A synonymous_variant 0.11
fbiB 3642084 p.Gly184Ser missense_variant 0.18
clpC1 4038741 p.Val655Ala missense_variant 0.29
clpC1 4038941 c.1764G>T synonymous_variant 0.4
clpC1 4039157 p.Lys516Asn missense_variant 0.17
clpC1 4040342 c.363C>T synonymous_variant 0.2
panD 4044207 c.75G>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245763 p.Gly844Val missense_variant 0.2
embB 4247907 p.Ile465Thr missense_variant 0.13
embB 4248719 p.Gly736Cys missense_variant 0.15
ethA 4326914 p.Ala187Val missense_variant 0.12
ethA 4328059 c.-586G>A upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0