TB-Profiler result

Run: SRR13068975
Summary

Run ID: SRR13068975

Sample name:

Date: 03-04-2023 08:11:57

Number of reads: 82337

Percentage reads mapped: 99.36

Strain: lineage4.9;lineage2

Drug-resistance: MDR-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
lineage2 East-Asian Beijing RD105 0.18
lineage4 Euro-American LAM;T;S;X;H None 0.95
lineage4.9 Euro-American (H37Rv-like) T1 None 0.97
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 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 9076 p.Arg592His missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491040 c.258C>T synonymous_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619833 c.-58T>C upstream_gene_variant 0.5
rpoB 762909 p.Ile1035Leu missense_variant 0.29
rpoC 763662 p.Ala98Val missense_variant 0.25
rpoC 764924 p.Gly519Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776564 c.1917C>T synonymous_variant 0.4
mmpR5 778990 p.Val1Met missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
Rv1258c 1406468 p.Met291Ile missense_variant 0.5
Rv1258c 1407068 c.273G>T synonymous_variant 0.67
rrs 1472156 n.311C>T non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
folC 2746170 p.Ala477Thr missense_variant 1.0
Rv2752c 3065358 p.Phe278Leu missense_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339086 c.-32G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240119 p.Val86Asp missense_variant 0.67
embA 4243346 c.114A>G synonymous_variant 1.0
embB 4247791 c.1278C>T synonymous_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326140 p.Glu445Val missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0