TB-Profiler result

Run: SRR11972416
Summary

Run ID: SRR11972416

Sample name:

Date: 03-04-2023 05:41:09

Number of reads: 795619

Percentage reads mapped: 99.46

Strain: lineage2.2.1.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 1.0
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 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Gly missense_variant 0.17 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
gyrB 6136 p.Glu299Asp missense_variant 0.33
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 490751 c.-32T>G upstream_gene_variant 0.33
fgd1 490981 p.Arg67Trp missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoB 759939 p.Pro45Thr missense_variant 1.0
rpoB 761378 c.1572C>T synonymous_variant 1.0
rpoB 762076 p.Lys757Arg missense_variant 0.5
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
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776288 c.2193C>T synonymous_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407416 c.-76C>G upstream_gene_variant 0.1
atpE 1460874 c.-171G>A upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472838 n.993A>G non_coding_transcript_exon_variant 0.22
rrs 1473333 n.1488T>C non_coding_transcript_exon_variant 0.2
rrl 1474038 n.382_384delAGT non_coding_transcript_exon_variant 0.17
rrl 1474553 n.896T>C non_coding_transcript_exon_variant 1.0
rrl 1476134 n.2477G>T non_coding_transcript_exon_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.22
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22
fabG1 1673361 c.-79C>G upstream_gene_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
inhA 1674267 c.66G>T synonymous_variant 0.12
rpsA 1834128 p.Ser196Cys missense_variant 0.25
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
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.17
Rv1979c 2222915 p.Ala84Thr missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
pepQ 2859604 p.Gly272Val missense_variant 0.13
thyX 3068153 c.-208G>T upstream_gene_variant 0.25
thyA 3074645 c.-174T>G upstream_gene_variant 0.6
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612383 p.Phe245Ser missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
ddn 3987002 c.161_162delGC frameshift_variant 0.18
embC 4241680 c.1818C>T synonymous_variant 0.13
embA 4242577 c.-656A>G upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248465 p.Ser651Asn missense_variant 0.26
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