TB-Profiler result

Run: SRR10272559
Summary

Run ID: SRR10272559

Sample name:

Date: 02-04-2023 16:37:57

Number of reads: 680962

Percentage reads mapped: 88.11

Strain: lineage4.4.1.1

Drug-resistance: Sensitive

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 0.98
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
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
fgd1 490751 c.-32T>G upstream_gene_variant 0.21
ccsA 619903 p.His5Asn missense_variant 0.15
rpoB 762771 p.Asn989Tyr missense_variant 0.15
rpoC 763901 p.Glu178Lys missense_variant 0.22
rpoC 765254 p.Val629Met missense_variant 0.22
rpoC 765361 c.1992C>T synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305062 p.Gly711Glu missense_variant 0.12
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.25
Rv1258c 1406152 p.Leu397Val missense_variant 0.13
Rv1258c 1406180 c.1161C>T synonymous_variant 0.15
Rv1258c 1406239 p.Gly368Ser missense_variant 0.12
Rv1258c 1406603 c.738G>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472719 n.874G>T non_coding_transcript_exon_variant 0.18
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.11
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.11
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.13
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.13
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.13
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.14
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.14
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.14
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918066 p.Ala43Pro missense_variant 0.4
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154161 p.Glu651Lys missense_variant 0.14
katG 2155016 p.Asp366Asn missense_variant 0.11
katG 2155917 c.195C>T synonymous_variant 0.13
PPE35 2168140 p.Ala825Thr missense_variant 0.12
PPE35 2168143 p.Phe824Leu missense_variant 0.12
PPE35 2168150 c.2463T>C synonymous_variant 0.12
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2221976 p.Ala397Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289019 p.Gly75Cys missense_variant 0.18
pncA 2289045 p.Ser66Leu missense_variant 0.22
kasA 2518437 p.Phe108Ser missense_variant 0.17
kasA 2519128 c.1014G>C synonymous_variant 0.25
kasA 2519131 c.1017G>C synonymous_variant 0.25
kasA 2519140 c.1026G>C synonymous_variant 0.25
kasA 2519143 c.1029G>C synonymous_variant 0.25
folC 2746745 p.Val285Gly missense_variant 0.43
folC 2747697 c.-99G>T upstream_gene_variant 0.22
pepQ 2859444 p.Glu325Asp missense_variant 0.17
thyX 3067459 p.Arg163Cys missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475182 c.1176C>T synonymous_variant 0.18
fprA 3475198 p.Phe398Leu missense_variant 0.15
Rv3236c 3612155 p.Arg321Leu missense_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiA 3640526 c.-16delG upstream_gene_variant 0.12
rpoA 3878639 c.-132C>G upstream_gene_variant 1.0
clpC1 4040021 c.684A>C synonymous_variant 0.12
clpC1 4040024 c.681A>G synonymous_variant 0.12
clpC1 4040027 c.678C>G synonymous_variant 0.14
embC 4242140 p.Asp760Tyr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245710 c.-804G>T upstream_gene_variant 0.13
embA 4246393 p.Trp1054* stop_gained 0.13
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.32
embB 4246556 p.Ala15Pro missense_variant 0.32
embB 4246567 c.54_55insT frameshift_variant 0.14
aftB 4268339 c.498G>A synonymous_variant 0.13
ethA 4326699 p.Arg259Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0