TB-Profiler result

Run: SRR10272563
Summary

Run ID: SRR10272563

Sample name:

Date: 02-04-2023 16:41:00

Number of reads: 928314

Percentage reads mapped: 91.19

Strain: lineage4.4.1.1

Drug-resistance: RR-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 0.99
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 761155 p.Ser450Leu missense_variant 0.14 rifampicin
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
mshA 575253 c.-95G>A upstream_gene_variant 0.25
mshA 575369 p.Asp8Asn missense_variant 0.25
mshA 576335 p.Pro330Ala missense_variant 0.2
mshA 576751 p.Lys468Asn missense_variant 0.33
ccsA 620669 p.Gly260Val missense_variant 0.25
rpoB 760498 p.Leu231Pro missense_variant 0.25
rpoB 760639 p.Gly278Asp missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778094 c.-896A>G upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304090 p.Asp387Gly missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155969 p.Leu48Pro missense_variant 0.11
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.11
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3068063 c.-118C>A upstream_gene_variant 0.13
thyA 3074514 c.-43T>G upstream_gene_variant 0.12
thyA 3074520 c.-50_-49insC upstream_gene_variant 0.12
thyA 3074528 c.-57T>C upstream_gene_variant 0.12
thyA 3074529 c.-58G>C upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473983 c.-24C>T upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612155 p.Arg321Leu missense_variant 1.0
Rv3236c 3612169 c.947delA frameshift_variant 0.15
Rv3236c 3612450 c.667C>T synonymous_variant 0.13
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
clpC1 4038987 c.1715_1717delGTG disruptive_inframe_deletion 0.17
clpC1 4038997 c.1708T>C synonymous_variant 0.18
clpC1 4039003 p.Asn568Asp missense_variant 0.18
clpC1 4039645 p.His354Asp missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243138 c.3279_3280delCG frameshift_variant 0.11
embA 4243589 c.357C>T synonymous_variant 0.33
embA 4245745 p.Pro838Gln missense_variant 0.14
embA 4246106 c.2878delC frameshift_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.27
embB 4246548 p.Pro12Gln missense_variant 0.21
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.21
embB 4246563 p.Leu17Trp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0