TB-Profiler result

Run: SRR18213931
Summary

Run ID: SRR18213931

Sample name:

Date: 03-04-2023 19:35:07

Number of reads: 2129647

Percentage reads mapped: 99.48

Strain: lineage3

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
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 4408100 c.102delG 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
gyrB 6963 p.Arg575His missense_variant 1.0
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 576560 c.1213C>T synonymous_variant 0.13
mshA 576623 p.Ala426Thr missense_variant 0.2
rpoB 759615 c.-192A>C upstream_gene_variant 0.13
rpoB 759620 c.-187A>C upstream_gene_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_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 776181 p.Asp767Ala missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304159 p.Val410Gly missense_variant 0.33
fbiC 1304472 c.1542T>C synonymous_variant 0.15
Rv1258c 1407001 p.Ala114Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 0.96
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339153 p.Leu12Phe missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841590 c.-170G>A upstream_gene_variant 0.99
clpC1 4038857 c.1848C>A synonymous_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242429 p.Ala856Asp missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247100 p.Ala196Val missense_variant 0.14
aftB 4268719 p.Asn40Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0