TB-Profiler result

Run: ERR2229367
Summary

Run ID: ERR2229367

Sample name:

Date: 31-03-2023 17:07:16

Number of reads: 1307107

Percentage reads mapped: 96.53

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
fgd1 490891 p.Val37Leu missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.22
rpoC 763376 p.Asp3Tyr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775760 c.2721C>T synonymous_variant 0.12
mmpL5 775813 p.Phe890Val missense_variant 0.14
mmpL5 775817 c.2664T>C synonymous_variant 0.12
mmpL5 775885 p.Ile866Val missense_variant 0.12
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.16
mmpL5 777128 c.1353A>G synonymous_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304963 p.Trp678Leu missense_variant 0.18
fbiC 1304976 p.Lys682Asn missense_variant 0.17
Rv1258c 1406290 p.Val351Leu missense_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 0.23
inhA 1674798 p.Met199Ile missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103020 p.Thr8Ile missense_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.19
PPE35 2167967 c.2646A>C synonymous_variant 0.19
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.66
PPE35 2170053 p.Thr187Ser missense_variant 0.66
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290133 c.-892C>A upstream_gene_variant 0.13
kasA 2518606 c.492G>C synonymous_variant 0.14
kasA 2518802 p.Phe230Val missense_variant 0.2
kasA 2518864 c.750G>C synonymous_variant 0.12
pepQ 2859931 p.Leu163Pro missense_variant 0.14
Rv2752c 3064964 p.Ala410Ser missense_variant 0.12
thyA 3074409 c.63C>A synonymous_variant 0.14
fbiD 3339744 c.627A>C synonymous_variant 0.18
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474041 p.Gly12Ala missense_variant 0.11
alr 3841082 c.339G>A synonymous_variant 0.12
alr 3841612 c.-193_-192insC upstream_gene_variant 0.18
rpoA 3878658 c.-151A>C upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244821 p.Gly530Val missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.42
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4247912 p.Val467Met missense_variant 0.11
ubiA 4269339 c.494delG frameshift_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 0.98
Rv3083 3448473 c.-30_*1408del transcript_ablation 1.0