TB-Profiler result

Run: ERR4814545

Summary

Run ID: ERR4814545

Sample name:

Date: 01-04-2023 13:21:16

Number of reads: 1034944

Percentage reads mapped: 99.23

Strain: lineage3.1.3

Drug-resistance: Other


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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
gid 4408125 c.77delT frameshift_variant 1.0 streptomycin
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
ccsA 620700 c.810C>G synonymous_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777164 p.Ser439Phe missense_variant 0.14
mmpL5 777875 c.606T>A synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407006 p.Leu112Arg missense_variant 0.17
embR 1417467 c.-120G>A upstream_gene_variant 0.11
atpE 1461186 p.Arg48Trp missense_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
ndh 2102106 c.936delC frameshift_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
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
pncA 2289455 c.-214G>C upstream_gene_variant 1.0
kasA 2518422 p.Val103Asp missense_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746876 c.723C>T synonymous_variant 1.0
Rv2752c 3065860 p.Leu111Arg missense_variant 1.0
thyX 3067490 c.456C>A synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474208 p.Glu68* stop_gained 0.12
alr 3841207 p.His72Tyr missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.22
clpC1 4039314 p.Arg464His missense_variant 0.14
embC 4241094 p.Cys411Phe missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249195 c.2682C>A synonymous_variant 1.0
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