TB-Profiler result

Run: SRR18003048
Summary

Run ID: SRR18003048

Sample name:

Date: 03-04-2023 19:15:28

Number of reads: 3360741

Percentage reads mapped: 81.89

Strain: lineage2.2.1

Drug-resistance: XDR-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 0.97
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
gyrB 6621 p.Asp461Ala missense_variant 0.93 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.96 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.89 linezolid
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2289105 p.Ala46Glu missense_variant 0.67 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol
pncA 2286220 c.-625_*2460del transcript_ablation 1.0 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.99
mshA 576108 p.Ala254Gly missense_variant 0.32
ccsA 620625 p.Ile245Met missense_variant 0.91
rpoB 761119 p.Asn438Ser missense_variant 0.96
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 0.98
mmpL5 776563 p.Glu640Lys missense_variant 0.95
mmpR5 779121 c.138_139dupTG frameshift_variant 0.93
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 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.1
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.15
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.1
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.1
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.13
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.15
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.21
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.16
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.21
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.16
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.21
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.18
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.18
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.18
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.17
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.23
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.23
rrl 1476506 n.2849T>C 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
pncA 2289893 c.-652C>T upstream_gene_variant 0.11
eis 2715568 c.-236G>A upstream_gene_variant 0.94
Rv2752c 3064826 p.Asp456Asn missense_variant 0.84
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
rpoA 3878599 c.-92C>G upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327307 p.Asp56Ala missense_variant 0.91
ethA 4328302 c.-829C>T upstream_gene_variant 0.91
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