TB-Profiler result

Run: SRR9588014

Summary

Run ID: SRR9588014

Sample name:

Date: 02-08-2023 15:27:49

Number of reads: NA

Percentage reads mapped: NA

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 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Asp missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8196 c.898delT frameshift_variant 0.15
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576315 p.Ala323Val missense_variant 0.15
ccsA 619710 c.-181G>T upstream_gene_variant 0.12
rpoB 759997 p.Trp64* stop_gained 0.13
rpoC 763516 p.Glu49Asp missense_variant 0.18
rpoC 763662 p.Ala98Val missense_variant 0.2
rpoC 764311 c.942C>T synonymous_variant 0.17
rpoC 766467 p.Glu1033Ala missense_variant 1.0
rpoC 766619 p.Gln1084Lys missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777132 p.Val450Ala missense_variant 0.12
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303161 c.234delC frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474642 n.985G>T non_coding_transcript_exon_variant 0.17
rrl 1474781 n.1124C>A non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2167916 c.2696delT frameshift_variant 0.2
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 0.92
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.25
PPE35 2170701 c.-89C>T upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518496 c.382C>T synonymous_variant 1.0
kasA 2519170 c.1056G>A synonymous_variant 0.11
eis 2714664 c.669C>T synonymous_variant 0.39
folC 2747518 c.80delT frameshift_variant 0.18
pepQ 2860176 c.243C>A synonymous_variant 0.11
Rv2752c 3065023 p.Pro390Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448522 p.Val7Phe missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3613089 c.27delT frameshift_variant 0.2
alr 3840625 p.Leu266Ile missense_variant 0.11
clpC1 4038853 p.Pro618Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
aftB 4268746 p.Gly31* stop_gained 0.25
ubiA 4269299 p.Ile179Val missense_variant 1.0
whiB6 4338286 c.235delG frameshift_variant 0.56
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408286 c.-84C>A upstream_gene_variant 0.11