TB-Profiler result

Run: ERR4812771
Summary

Run ID: ERR4812771

Sample name:

Date: 01-04-2023 12:19:23

Number of reads: 525217

Percentage reads mapped: 92.36

Strain: lineage2.2.1

Drug-resistance: RR-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 0.17
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.1
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 0.5 rifampicin
pncA 2289090 p.His51Arg missense_variant 0.8 pyrazinamide
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 8040 p.Gly247Ser missense_variant 0.85
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490928 p.Gly49Asp missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 0.43
mshA 575907 p.Ala187Val missense_variant 0.62
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.2
rpoC 763546 c.177A>G synonymous_variant 0.11
rpoC 763570 c.201G>C synonymous_variant 0.14
rpoC 763573 c.204G>C synonymous_variant 0.13
rpoC 763594 c.225C>T synonymous_variant 0.2
rpoC 763633 c.264T>C synonymous_variant 0.27
rpoC 763660 c.291T>G synonymous_variant 0.15
rpoC 763666 c.297G>T synonymous_variant 0.15
rpoC 763675 c.306C>G synonymous_variant 0.15
rpoC 764632 c.1263T>A synonymous_variant 0.22
rpoC 764756 p.Leu463Met missense_variant 0.12
rpoC 764764 c.1395T>C synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.75
rpoC 766487 p.Pro1040Ala missense_variant 0.56
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.38
mmpL5 778362 p.Leu40* stop_gained 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 0.3
mmpS5 779630 c.-725T>C upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.33
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.4
rrs 1472188 n.343A>G non_coding_transcript_exon_variant 0.33
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.4
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.5
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.18
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.18
rpsA 1834683 p.Ala381Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.7
PPE35 2168434 p.Gly727Arg missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290051 c.-810C>T upstream_gene_variant 0.15
kasA 2518919 p.Gly269Ser missense_variant 0.67
ahpC 2726441 c.249G>T synonymous_variant 0.17
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.33
thyX 3068101 c.-156G>A upstream_gene_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.45
thyA 3074495 c.-24C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449663 p.Ile387Asn missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.92
fprA 3474059 p.Ala18Val missense_variant 0.15
fprA 3474452 p.Arg149Leu missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044129 c.153C>T synonymous_variant 0.25
embC 4242182 p.Ala774Ser missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.25
embB 4249497 p.Pro995Leu missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.2
ubiA 4269864 c.-32delG upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.36
gid 4407927 p.Glu92Asp missense_variant 0.38
gid 4408156 p.Leu16Arg missense_variant 0.67