TB-Profiler result

Run: ERR2747596
Summary

Run ID: ERR2747596

Sample name:

Date: 31-03-2023 23:27:41

Number of reads: 104230

Percentage reads mapped: 26.18

Strain: lineage4.9

Drug-resistance: RR-TB

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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
La1.8.1 M.bovis None None 0.11
lineage4.9 Euro-American (H37Rv-like) T1 None 0.94
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
rpoB 761089 p.Ser428Ile missense_variant 1.0 rifampicin
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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
rpoC 764322 p.Pro318Leu missense_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
pncA 2289041 c.201G>A synonymous_variant 0.29
kasA 2518132 c.18C>T synonymous_variant 1.0
ribD 2987209 p.Gly124Asp missense_variant 0.67
Rv2752c 3065988 p.Glu68Asp missense_variant 1.0
Rv3083 3449724 c.1221C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840938 c.483G>A synonymous_variant 0.5
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040125 p.Glu194* stop_gained 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embC 4242981 p.Met1040Thr missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247344 c.831C>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0