TB-Profiler result

Run: SRR7645854
Summary

Run ID: SRR7645854

Sample name:

Date: 04-04-2023 19:55:00

Number of reads: 1541089

Percentage reads mapped: 99.71

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.97
lineage4.4.1 Euro-American (S-type) S;T None 0.98
lineage4.4.1.1 Euro-American S;Orphans None 0.98
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 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2288763 p.Thr160Arg missense_variant 0.97 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407727 c.475delA frameshift_variant 0.92 streptomycin
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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576276 p.Asp310Gly missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777140 c.1341G>C synonymous_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475311 n.1654G>T non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 0.96
PPE35 2170122 p.Ala164Val missense_variant 0.12
Rv1979c 2222341 p.Met275Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289106 p.Ala46Ser missense_variant 0.11
ribD 2987483 c.645C>A synonymous_variant 0.12
Rv2752c 3064741 p.Gly484Ala missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.95
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641010 c.-525C>T upstream_gene_variant 0.91
clpC1 4040711 c.-7G>T upstream_gene_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245512 c.2280G>C synonymous_variant 1.0
aftB 4267746 p.Ser364* stop_gained 0.12
aftB 4267846 p.Gly331Ser missense_variant 0.18
aftB 4267853 c.984G>A synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0