TB-Profiler result

Run: SRR19428574
Summary

Run ID: SRR19428574

Sample name:

Date: 03-04-2023 21:40:37

Number of reads: 679691

Percentage reads mapped: 99.29

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
gyrB 5566 p.Phe109Leu missense_variant 0.12
gyrB 5610 p.Gly124Asp missense_variant 0.12
gyrB 5701 c.466dupC frameshift_variant 0.13
gyrB 6266 p.Pro343Thr missense_variant 0.14
gyrA 6817 c.-485G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7524 p.Arg75Trp missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.94
rpoB 761573 c.1767C>T synonymous_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777280 p.Ala401Ser missense_variant 0.14
mmpL5 777613 p.Gly290Trp missense_variant 0.12
mmpL5 778973 c.-493T>C upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472667 n.822T>C non_coding_transcript_exon_variant 0.12
rrs 1472685 n.840G>A non_coding_transcript_exon_variant 0.13
rrs 1472769 n.924C>A non_coding_transcript_exon_variant 0.2
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.14
rpsA 1833454 c.-88G>T upstream_gene_variant 0.12
rpsA 1834468 c.927A>G synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102592 c.449_450dupGC frameshift_variant 0.12
katG 2154084 c.2028G>T synonymous_variant 0.2
katG 2154731 p.Gln461Glu missense_variant 0.13
PPE35 2167760 c.2853G>T synonymous_variant 0.13
PPE35 2168204 c.2409G>A synonymous_variant 0.13
PPE35 2168233 p.Ile794Val missense_variant 0.18
PPE35 2169158 p.Leu485Phe missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518771 c.657C>A synonymous_variant 0.13
folC 2747585 p.Asn5Ser missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074363 p.Asp37Tyr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449147 p.Ser215Trp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612546 p.Ala191Ser missense_variant 0.14
Rv3236c 3612905 p.Leu71Ser missense_variant 0.11
Rv3236c 3612970 p.Leu49Phe missense_variant 0.13
alr 3840296 c.1125G>A synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044228 c.54C>T synonymous_variant 0.12
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4241443 c.1581C>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.1
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4249491 p.Ala993Val missense_variant 0.12
embB 4249669 c.3156C>T synonymous_variant 0.12
ethA 4327233 p.Ile81Val missense_variant 0.1
whiB6 4338333 c.189A>G synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0