TB-Profiler result

Run: ERR4829916
Summary

Run ID: ERR4829916

Sample name:

Date: 01-04-2023 19:45:57

Number of reads: 3333310

Percentage reads mapped: 98.49

Strain: lineage4.8;lineage4.1.2.1

Drug-resistance: MDR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.24
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.78
lineage4.1.2 Euro-American T;H None 0.24
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.24
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 761101 p.Gln432Pro missense_variant 0.25 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.24 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.22 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.2 ethambutol
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 6639 p.Ala467Val missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 0.25
fgd1 491591 p.Lys270Met missense_variant 0.32
mshA 575679 p.Asn111Ser missense_variant 0.23
rpoB 760115 c.309C>T synonymous_variant 0.21
rpoC 764817 p.Val483Gly missense_variant 0.22
rpoC 765150 p.Gly594Glu missense_variant 0.3
rpoC 766085 p.Pro906Ala missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777820 c.661C>T synonymous_variant 0.26
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>C upstream_gene_variant 0.81
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.8
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221897 p.Val423Ala missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.25
alr 3840764 c.657G>C synonymous_variant 0.8
rpoA 3878432 c.76C>T synonymous_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407970 p.Pro78Gln missense_variant 0.21