TB-Profiler result

Run: ERR4799636
Summary

Run ID: ERR4799636

Sample name:

Date: 01-04-2023 09:15:41

Number of reads: 3339397

Percentage reads mapped: 76.08

Strain: lineage2.2.1

Drug-resistance: Pre-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 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.97
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7570 p.Ala90Val missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.99 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.99 ethambutol
embB 4247429 p.Met306Val missense_variant 0.97 ethambutol
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
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
Rv1258c 1406760 c.580_581insC frameshift_variant 0.93
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.21
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.21
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.22
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.22
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.22
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.22
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.21
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.21
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.22
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.22
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.22
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.23
rrs 1472993 n.1148G>A non_coding_transcript_exon_variant 0.22
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.23
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.23
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.24
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.23
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.22
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.16
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.16
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.15
rrl 1476417 n.2760T>C non_coding_transcript_exon_variant 0.14
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.16
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
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
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.99
whiB7 3568854 c.-176delG upstream_gene_variant 0.98
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 0.99
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326513 p.Thr321Pro missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.97