TB-Profiler result

Run: ERR1665405
Summary

Run ID: ERR1665405

Sample name:

Date: 31-03-2023 14:55:06

Number of reads: 2308038

Percentage reads mapped: 95.87

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.16 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289207 p.Asp12Gly missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
embB 4247574 p.Asp354Ala missense_variant 0.99 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 1.0 ethionamide
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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_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
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 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.19
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.22
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.25
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.24
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.22
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.22
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.21
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.21
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.22
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.25
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.21
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.21
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.23
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.18
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.18
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.13
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.13
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.15
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.15
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.17
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.17
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.13
rrl 1474674 n.1017A>C non_coding_transcript_exon_variant 0.14
rrl 1474675 n.1018C>A non_coding_transcript_exon_variant 0.21
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.14
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.14
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.17
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.17
rrl 1474723 n.1066G>A non_coding_transcript_exon_variant 0.13
rrl 1474732 n.1075A>T non_coding_transcript_exon_variant 0.19
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.31
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.12
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.29
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.2
rrl 1474783 n.1126G>T non_coding_transcript_exon_variant 0.2
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.19
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.24
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.13
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.17
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.11
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.11
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.11
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.12
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.12
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.1
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.1
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
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
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338563 c.-42G>T upstream_gene_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