TB-Profiler result

Run: ERR9993028
Summary

Run ID: ERR9993028

Sample name:

Date: 02-04-2023 14:00:32

Number of reads: 3776186

Percentage reads mapped: 73.59

Strain: lineage2.2.2

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4248002 p.Gln497Lys missense_variant 0.99 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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 576108 p.Ala254Gly missense_variant 0.34
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779412 c.424dupC frameshift_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305485 p.Ala852Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.11
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.18
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.27
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.27
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.27
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.27
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.28
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.26
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.25
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.24
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.24
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.24
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.23
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.23
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.24
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.18
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.18
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.18
rrs 1472669 n.824_825insTGG non_coding_transcript_exon_variant 0.12
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.12
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.13
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.17
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.18
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.2
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.2
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.2
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.21
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.2
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.21
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.2
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.2
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.2
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.2
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.18
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.2
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.2
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.2
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.19
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.18
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.18
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.17
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.18
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.18
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.18
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 2221939 p.Arg409Gln 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
embB 4246584 p.Arg24Pro missense_variant 0.12
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