TB-Profiler result

Run: ERR5987372

Summary

Run ID: ERR5987372

Sample name:

Date: 02-04-2023 01:33:55

Number of reads: 3998137

Percentage reads mapped: 99.54

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 0.99
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 7570 p.Ala90Val 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
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 1.0 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
gyrB 6001 c.762G>A synonymous_variant 0.29
gyrB 6209 p.Leu324Met missense_variant 0.11
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9383 c.2082T>C synonymous_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491759 p.Ser326Leu missense_variant 0.12
rpoB 761425 p.Ser540* stop_gained 0.15
rpoB 762281 c.2475G>A synonymous_variant 0.12
rpoB 762496 p.Asp897Val missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765597 p.Lys743Met missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776261 c.2220C>T synonymous_variant 0.14
mmpL5 777625 p.Gln286Lys missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304817 c.1887T>C synonymous_variant 0.14
Rv1258c 1406527 p.Leu272Met missense_variant 0.15
Rv1258c 1407502 c.-162G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.11
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.11
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.1
rrl 1473446 n.-211delG upstream_gene_variant 0.15
rrl 1474160 n.503C>T non_coding_transcript_exon_variant 0.12
rrl 1474968 n.1311G>A non_coding_transcript_exon_variant 0.13
fabG1 1673598 p.Lys53Asn missense_variant 0.25
inhA 1674692 p.Ala164Val missense_variant 0.14
rpsA 1833442 c.-100G>A upstream_gene_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834779 p.Glu413Gly missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102052 p.Gly331Cys missense_variant 0.14
katG 2154017 p.Gly699Arg missense_variant 0.13
katG 2154067 p.Asp682Val missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155254 c.858C>A synonymous_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167962 p.Gly884Glu missense_variant 0.14
PPE35 2168638 p.Pro659Thr missense_variant 0.12
PPE35 2169970 p.Gly215Cys missense_variant 0.13
Rv1979c 2221899 c.1266C>T synonymous_variant 0.14
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2222508 c.657G>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518078 c.-37T>C upstream_gene_variant 0.2
kasA 2518146 c.36delC frameshift_variant 0.17
kasA 2518555 c.441C>A synonymous_variant 0.12
eis 2715243 c.90T>C synonymous_variant 0.11
ahpC 2726604 p.Val138Ile missense_variant 0.12
ahpC 2726727 p.Arg179Gly missense_variant 0.2
folC 2747015 p.Thr195Asn missense_variant 0.2
folC 2747297 c.301dupC frameshift_variant 0.17
pepQ 2859726 c.693C>A synonymous_variant 0.14
ribD 2986986 p.Asp50Tyr missense_variant 0.17
thyX 3068142 c.-197G>A upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338926 c.-191delC upstream_gene_variant 0.12
Rv3083 3448695 p.Tyr64* stop_gained 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474888 c.882G>A synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613170 c.-54G>T upstream_gene_variant 0.18
ddn 3986709 c.-135G>A upstream_gene_variant 0.13
clpC1 4039048 p.Gly553Cys missense_variant 0.18
embC 4240305 p.Leu148Pro missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245758 c.-756C>T upstream_gene_variant 0.13
embB 4246928 p.Gln139* stop_gained 0.12
embB 4247739 p.Ala409Glu missense_variant 0.12
aftB 4267241 c.1596G>A synonymous_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