TB-Profiler result

Run: SRR16088013
Summary

Run ID: SRR16088013

Sample name:

Date: 03-04-2023 16:03:44

Number of reads: 3304219

Percentage reads mapped: 99.61

Strain: lineage4.1.2.1;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.89
lineage4 Euro-American LAM;T;S;X;H None 0.14
lineage4.1 Euro-American T;X;H None 0.12
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.89
lineage4.1.2 Euro-American T;H None 0.12
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.88
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.12
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 0.86
mshA 575679 p.Asn111Ser missense_variant 0.14
mshA 575907 p.Ala187Val missense_variant 0.86
mshA 576108 p.Ala254Gly missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 0.83
rpoB 760115 c.309C>T synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.9
rpoC 765150 p.Gly594Glu missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 0.89
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
mmpL5 776182 p.Asp767Asn missense_variant 0.91
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.9
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.86
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.88
PPE35 2167926 p.Leu896Ser missense_variant 0.89
PPE35 2170065 p.Ala183Gly missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.14
pepQ 2860159 p.Ala87Gly missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.16
Rv3236c 3612813 p.Thr102Ala missense_variant 0.88
rpoA 3878637 c.-130G>C upstream_gene_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.29
clpC1 4039896 p.Lys270Arg missense_variant 0.93
embC 4240409 p.Pro183Ala missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.88
embB 4246584 p.Arg24Pro missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.81
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.9
gid 4407927 p.Glu92Asp missense_variant 0.9
gid 4408343 c.-141C>G upstream_gene_variant 0.13