TB-Profiler result

Run: SRR7645864
Summary

Run ID: SRR7645864

Sample name:

Date: 04-04-2023 19:55:35

Number of reads: 993215

Percentage reads mapped: 99.66

Strain: lineage4.4.1.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
katG 2154853 p.Met420Thr missense_variant 0.1 isoniazid
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 0.95
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576355 c.1008G>A synonymous_variant 0.11
ccsA 619965 c.75G>A synonymous_variant 0.17
ccsA 620389 c.500delT frameshift_variant 0.1
ccsA 620794 c.906delC frameshift_variant 0.15
rpoC 763217 c.-153G>A upstream_gene_variant 0.15
rpoC 764264 p.Val299Ile missense_variant 0.22
rpoC 765234 p.Ala622Val missense_variant 0.12
rpoC 765849 p.Pro827Gln missense_variant 0.11
mmpL5 775626 p.Trp952Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303666 p.Thr246Pro missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474685 n.1028G>A non_coding_transcript_exon_variant 0.11
rpsA 1833429 c.-112delT upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169002 c.1611G>A synonymous_variant 0.13
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2222832 c.333T>C synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519343 p.Ala410Val missense_variant 0.25
folC 2746899 p.Ile234Val missense_variant 1.0
folC 2747428 c.171G>T synonymous_variant 0.18
folC 2747588 p.Thr4Arg missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086971 p.Lys51Arg missense_variant 0.12
Rv3083 3448368 c.-136C>T upstream_gene_variant 0.11
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448878 c.375C>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641493 c.-42T>C upstream_gene_variant 0.33
fbiB 3641657 c.123C>A synonymous_variant 0.11
alr 3841112 p.Asp103Glu missense_variant 0.12
alr 3841608 c.-188A>G upstream_gene_variant 1.0
clpC1 4040522 c.183T>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243148 c.-85A>T upstream_gene_variant 0.17
embA 4246230 p.Ala1000Thr missense_variant 0.18
embB 4247171 c.658C>T synonymous_variant 0.12
embB 4248828 p.Gly772Asp missense_variant 0.14
embB 4249106 p.Leu865Met missense_variant 0.12
aftB 4267655 c.1181delG frameshift_variant 0.19
ubiA 4269125 p.Ala237Thr missense_variant 0.13
ethA 4327355 p.Ser40Phe missense_variant 0.12
ethA 4327440 p.Ala12Thr missense_variant 0.18
ethR 4327603 p.Arg19Trp missense_variant 0.15
ethA 4327995 c.-522C>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0