TB-Profiler result

Run: SRR16088237
Summary

Run ID: SRR16088237

Sample name:

Date: 03-04-2023 16:05:00

Number of reads: 3792764

Percentage reads mapped: 99.74

Strain: lineage4.3.3;lineage2.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 0.96
lineage4.3 Euro-American (LAM) mainly-LAM None 0.9
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.07
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.07
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.92
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.14 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 7058 p.Ile607Val missense_variant 0.88
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.82
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.27
mshA 576456 p.Val370Gly missense_variant 0.28
mshA 576613 c.1266A>C synonymous_variant 0.3
mshA 576616 c.1269G>C synonymous_variant 0.31
ccsA 620625 p.Ile245Met missense_variant 0.13
rpoC 764367 p.Gly333Ala missense_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 0.93
rpoC 766645 p.Glu1092Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.9
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.32
rpsA 1834177 c.636A>C synonymous_variant 0.13
rpsA 1834836 p.Met432Thr missense_variant 0.9
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.87
PPE35 2170065 p.Ala183Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.91
kasA 2519071 p.Asp319Glu missense_variant 0.22
folC 2746340 p.Ala420Val missense_variant 0.93
pepQ 2860159 p.Ala87Gly missense_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 0.91
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.47
fbiD 3339746 p.Ala210Gly missense_variant 0.43
fbiD 3339751 p.Ala212Pro missense_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.42
whiB7 3568431 c.249C>G synonymous_variant 0.16
rpoA 3878597 c.-90G>C upstream_gene_variant 0.62
rpoA 3878609 c.-102T>C upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.73
clpC1 4038287 c.2418C>T synonymous_variant 0.94
clpC1 4038968 c.1737G>A synonymous_variant 0.93
embC 4240409 p.Pro183Ala missense_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.46
embB 4246529 p.Ser6Arg missense_variant 0.33
embB 4247016 p.Ser168Trp missense_variant 0.19
embB 4247020 c.507C>G synonymous_variant 0.18
embB 4248328 c.1815G>C synonymous_variant 0.25
aftB 4268566 p.Ser91Ala missense_variant 0.88
whiB6 4338200 p.Asp108His missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.15
gid 4408156 p.Leu16Arg missense_variant 0.9