TB-Profiler result

Run: ERR4813498
Summary

Run ID: ERR4813498

Sample name:

Date: 01-04-2023 12:47:21

Number of reads: 2505418

Percentage reads mapped: 98.78

Strain: lineage4.1.1;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
lineage2 East-Asian Beijing RD105 0.1
lineage4 Euro-American LAM;T;S;X;H None 0.88
lineage4.1 Euro-American T;X;H None 0.89
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.16
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.06
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.89
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 0.17 streptomycin
ethA 4327465 c.8delA frameshift_variant 0.15 ethionamide, ethionamide
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 6052 p.Ile271Met missense_variant 0.83
gyrB 7005 p.Gly589Val missense_variant 0.18
gyrB 7221 p.Ser661Thr missense_variant 0.87
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 0.22
mshA 575729 p.Gln128Lys missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.15
PPE35 2170273 p.Arg114Cys missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067945 p.Val1Met missense_variant 0.7
thyA 3074588 c.-117A>G upstream_gene_variant 0.78
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
rpoA 3878554 c.-47C>A upstream_gene_variant 0.14
clpC1 4039958 c.747G>A synonymous_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.91
embA 4243460 c.228C>T synonymous_variant 0.1
embA 4243661 c.429C>T synonymous_variant 0.12
embA 4244371 p.Arg380His missense_variant 0.12
embB 4246584 p.Arg24Pro missense_variant 0.25
embB 4247033 p.Ser174Arg missense_variant 0.29
embB 4247709 p.Asn399Thr missense_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 0.92
ethA 4326116 p.Thr453Ile missense_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 0.13