TB-Profiler result

Run: ERR6865942
Summary

Run ID: ERR6865942

Sample name:

Date: 02-04-2023 03:10:23

Number of reads: 2493799

Percentage reads mapped: 99.53

Strain: lineage4.8;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 0.22
lineage4 Euro-American LAM;T;S;X;H None 0.79
lineage4.1 Euro-American T;X;H None 0.51
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.24
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.24
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.26
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.51
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 4407880 p.Leu108Arg missense_variant 0.58 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 6052 p.Ile271Met missense_variant 0.46
gyrB 7221 p.Ser661Thr missense_variant 0.54
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.73
gyrA 9304 p.Gly668Asp missense_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 0.28
mshA 575907 p.Ala187Val missense_variant 0.23
ccsA 620625 p.Ile245Met missense_variant 0.24
rpoC 763031 c.-339T>C upstream_gene_variant 0.22
rpoC 765150 p.Gly594Glu missense_variant 0.48
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.23
mmpL5 776182 p.Asp767Asn missense_variant 0.23
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.21
embR 1416699 p.Leu217Val missense_variant 0.56
embR 1416748 p.Glu200Asp missense_variant 0.56
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.19
PPE35 2167926 p.Leu896Ser missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715565 c.-233C>T upstream_gene_variant 0.23
thyA 3074588 c.-117A>G upstream_gene_variant 0.68
ald 3086788 c.-32T>C upstream_gene_variant 0.79
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.77
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24
alr 3840764 c.657G>C synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.48
embA 4243460 c.228C>T synonymous_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 0.44
aftB 4267647 p.Asp397Gly missense_variant 0.17
ethA 4326116 p.Thr453Ile missense_variant 0.47
whiB6 4338409 p.Pro38Leu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.34
gid 4407927 p.Glu92Asp missense_variant 0.29