TB-Profiler result

Run: ERR2513941

Summary

Run ID: ERR2513941

Sample name:

Date: 31-03-2023 20:00:45

Number of reads: 833883

Percentage reads mapped: 99.41

Strain: lineage3.1.3

Drug-resistance: Sensitive


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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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1.3 East-African-Indian CAS RD750 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 491742 c.960T>C synonymous_variant 1.0
mshA 576750 p.Lys468Thr missense_variant 0.25
ccsA 619901 p.Leu4Pro missense_variant 0.12
ccsA 620529 c.639G>C synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764541 p.Val391Gly missense_variant 0.11
rpoC 764543 p.Thr392Asp missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775987 p.His832Tyr missense_variant 0.12
mmpL5 775990 c.2491C>T synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778049 c.-941G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834159 c.618G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154648 c.1464G>A synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169902 c.711G>A synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.1
PPE35 2170066 p.Ala183Thr missense_variant 0.11
Rv1979c 2222732 c.432delT frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2517997 c.-118A>C upstream_gene_variant 0.11
kasA 2518578 p.Gly155Asp missense_variant 0.11
kasA 2518998 p.Leu295Pro missense_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.11
kasA 2519143 c.1029G>C synonymous_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyA 3074212 p.Thr87Ile missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878052 c.456C>T synonymous_variant 0.12
clpC1 4039829 p.Leu292Ile missense_variant 0.27
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242396 p.Pro845Leu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246993 p.Asn160Lys missense_variant 0.1
embB 4249195 c.2682C>A synonymous_variant 1.0
aftB 4267139 c.1698G>A synonymous_variant 1.0
aftB 4267801 c.1036T>C synonymous_variant 0.12
aftB 4268457 p.Ala127Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408175 p.Ala10Pro missense_variant 1.0