TB-Profiler result

Run: SRR9588015
Summary

Run ID: SRR9588015

Sample name:

Date: 02-08-2023 15:29:13

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 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491316 c.534C>G synonymous_variant 0.12
mshA 576734 c.1387C>T synonymous_variant 0.13
ccsA 620619 c.729G>A synonymous_variant 0.11
rpoC 766467 p.Glu1033Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777042 c.1438delC frameshift_variant 0.1
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801143 p.Val112Ala missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
rpsA 1833726 p.Val62Ala missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518496 c.382C>T synonymous_variant 1.0
eis 2715354 c.-22G>A upstream_gene_variant 0.11
folC 2747608 c.-10C>A upstream_gene_variant 0.1
pepQ 2859944 p.Ala159Ser missense_variant 0.14
ribD 2986911 p.Asp25Asn missense_variant 0.12
ribD 2987404 p.Arg189Leu missense_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
Rv3083 3448748 p.Arg82Gln missense_variant 0.12
Rv3083 3449105 p.Pro201His missense_variant 0.22
Rv3083 3449552 p.Ile350Thr missense_variant 0.1
Rv3083 3449606 p.Pro368Leu missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474802 p.Arg266Gly missense_variant 0.12
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244847 p.Gly539Cys missense_variant 0.2
embA 4244984 p.Leu584Phe missense_variant 0.12
embB 4249425 p.Leu971Pro missense_variant 0.11
aftB 4268888 c.-52C>A upstream_gene_variant 0.14
ubiA 4269299 p.Ile179Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408034 c.168_169insCG frameshift_variant 0.13