TB-Profiler result

Run: ERR2515304
Summary

Run ID: ERR2515304

Sample name:

Date: 31-03-2023 20:51:47

Number of reads: 728918

Percentage reads mapped: 93.55

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 0.99
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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.91 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2289220 p.Asp8Asn missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethR 4327831 p.Ala95Thr missense_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 763555 c.186C>T synonymous_variant 0.93
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 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304658 c.1728C>G synonymous_variant 0.12
fbiC 1304660 p.Tyr577Phe missense_variant 0.12
fbiC 1304664 c.1734G>C synonymous_variant 0.12
fbiC 1304671 p.Val581Thr missense_variant 0.12
fbiC 1304676 c.1746A>C synonymous_variant 0.12
fbiC 1304691 c.1761G>T synonymous_variant 0.12
fbiC 1304694 c.1764A>G synonymous_variant 0.12
fbiC 1304715 c.1785G>C synonymous_variant 0.15
fbiC 1304724 c.1794A>G synonymous_variant 0.15
fbiC 1304727 c.1797A>C synonymous_variant 0.14
fbiC 1304742 c.1812T>C synonymous_variant 0.16
fbiC 1304751 c.1821C>G synonymous_variant 0.17
fbiC 1304757 c.1827A>G synonymous_variant 0.19
fbiC 1304760 c.1830G>C synonymous_variant 0.19
fbiC 1304769 c.1839C>G synonymous_variant 0.19
fbiC 1304781 c.1851G>C synonymous_variant 0.15
fbiC 1304784 c.1854T>C synonymous_variant 0.15
fbiC 1304790 c.1860C>G synonymous_variant 0.14
fbiC 1304811 c.1881C>G synonymous_variant 0.14
fbiC 1304817 c.1887T>C synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.12
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.12
rrs 1472456 n.611T>C non_coding_transcript_exon_variant 0.11
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.11
rrl 1474969 n.1312G>T non_coding_transcript_exon_variant 0.14
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.17
rrl 1475062 n.1405A>G non_coding_transcript_exon_variant 0.17
rrl 1475479 n.1822C>G non_coding_transcript_exon_variant 0.12
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.13
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
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
rpoA 3878103 c.405A>G synonymous_variant 0.12
clpC1 4039979 c.726C>G synonymous_variant 0.11
clpC1 4040009 c.696C>G synonymous_variant 0.12
clpC1 4040015 c.690G>C synonymous_variant 0.12
clpC1 4040021 c.684A>C synonymous_variant 0.13
clpC1 4040024 c.681A>G synonymous_variant 0.13
clpC1 4040033 c.672G>T synonymous_variant 0.12
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 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