TB-Profiler result

Run: SRR18002899
Summary

Run ID: SRR18002899

Sample name:

Date: 03-04-2023 19:08:50

Number of reads: 5334689

Percentage reads mapped: 97.58

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 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
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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
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 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.41
ccsA 620625 p.Ile245Met missense_variant 1.0
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
mmpR5 779165 p.Ala59Val missense_variant 0.99
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.13
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.17
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.29
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.29
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.2
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.2
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.2
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.2
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.2
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.22
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.16
rrl 1474581 n.924C>T non_coding_transcript_exon_variant 0.15
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.4
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.5
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.5
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.5
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.5
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.5
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.5
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.5
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.43
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.43
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.43
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.29
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.33
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.25
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.25
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.17
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.18
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.18
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.18
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.18
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.15
rrl 1475940 n.2283C>T non_coding_transcript_exon_variant 0.13
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.12
rrl 1476368 n.2711T>A non_coding_transcript_exon_variant 0.12
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
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 2170690 c.-78A>C upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_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
embC 4242486 p.Glu875Gly missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embB 4246543 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.19
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.24
embB 4246567 c.54G>T synonymous_variant 0.25
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