TB-Profiler result

Run: ERR2229139
Summary

Run ID: ERR2229139

Sample name:

Date: 31-03-2023 16:43:53

Number of reads: 891191

Percentage reads mapped: 97.96

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 5788 c.549G>C synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491336 p.Ala185Val missense_variant 0.14
fgd1 491716 p.Ala312Pro missense_variant 0.13
rpoC 766981 c.3612T>C synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775735 p.Phe916Leu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303562 c.635delG frameshift_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304822 p.His631Arg missense_variant 0.11
embR 1416890 p.Leu153Pro missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476686 n.3029C>T non_coding_transcript_exon_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
rpsA 1834964 c.1428delA frameshift_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154699 p.Gln471His missense_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2167973 c.2640A>G synonymous_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.55
PPE35 2170053 p.Thr187Ser missense_variant 0.52
Rv1979c 2223010 p.Val52Gly missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714773 p.Pro187Leu missense_variant 0.18
pepQ 2859733 p.Tyr229Phe missense_variant 0.15
pepQ 2860186 p.Ala78Val missense_variant 0.22
pepQ 2860259 p.Leu54Met missense_variant 0.14
fbiD 3339734 p.Ala206Gly missense_variant 0.13
alr 3840341 c.1080C>G synonymous_variant 0.18
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4039054 p.Phe551Leu missense_variant 0.17
panD 4044289 c.-8A>T upstream_gene_variant 0.12
panD 4044350 c.-69C>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243083 p.Asp1074Ala missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.75
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4247073 p.Gly187Glu missense_variant 0.18
ethA 4326885 p.Ser197Pro missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0