TB-Profiler result

Run: ERR2229102
Summary

Run ID: ERR2229102

Sample name:

Date: 31-03-2023 16:39:04

Number of reads: 1480262

Percentage reads mapped: 99.21

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 576108 p.Ala254Gly missense_variant 0.33
mshA 576576 p.Ala410Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
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 0.18
tlyA 1917966 c.27C>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102919 p.Leu42Met missense_variant 0.12
PPE35 2167745 c.2868C>G synonymous_variant 0.14
PPE35 2167865 c.2748G>C synonymous_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.16
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987003 c.165C>A synonymous_variant 0.18
ribD 2987452 p.Arg205His missense_variant 0.25
Rv3083 3448488 c.-16C>T upstream_gene_variant 0.18
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.29
clpC1 4040411 c.294T>G synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246531 p.Ser6Arg missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.16
embB 4246555 c.42G>C synonymous_variant 0.19
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246567 c.54G>T synonymous_variant 0.21
aftB 4268578 p.Ala87Ser missense_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0