TB-Profiler result

Run: SRR18002996

Summary

Run ID: SRR18002996

Sample name:

Date: 03-04-2023 19:13:16

Number of reads: 3925221

Percentage reads mapped: 97.32

Strain: lineage2.2.2

Drug-resistance: MDR-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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.99
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 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 0.97 ethambutol
gid 4408087 c.115delC frameshift_variant 0.96 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
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 1.0
mshA 576108 p.Ala254Gly missense_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460858 c.-187C>T upstream_gene_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.29
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.25
rrl 1474849 n.1192G>T non_coding_transcript_exon_variant 0.12
rrl 1475235 n.1582dupA non_coding_transcript_exon_variant 0.18
rrl 1476319 n.2662C>T non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.11
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.11
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.16
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.11
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.16
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.16
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.12
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.12
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.14
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747196 p.Asp135Asn missense_variant 1.0
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 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.13
embB 4246556 p.Ala15Pro missense_variant 0.13
embB 4246563 p.Leu17Trp missense_variant 0.13
embB 4246567 c.54G>T synonymous_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0