TB-Profiler result

Run: ERR4831976
Summary

Run ID: ERR4831976

Sample name:

Date: 01-04-2023 21:14:43

Number of reads: 457737

Percentage reads mapped: 99.6

Strain: lineage2.2.1.1

Drug-resistance: MDR-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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288943 c.298dupA frameshift_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrB 5882 c.645delA frameshift_variant 0.1
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 9629 c.2328C>T synonymous_variant 0.11
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
ccsA 620748 c.858T>G synonymous_variant 0.36
rpoB 760057 p.Leu84Pro missense_variant 0.15
rpoB 760163 p.Lys119Asn missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766868 p.Ile1167Val missense_variant 0.15
rpoC 767052 p.Glu1228Gly missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776397 p.Val695Ala missense_variant 0.12
mmpL5 777970 p.Thr171Ala missense_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.25
fbiC 1304637 c.1707G>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475284 n.1627C>G non_coding_transcript_exon_variant 1.0
fabG1 1673464 p.Ala9Thr missense_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
PPE35 2168088 p.Pro842Gln missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519139 p.Ala342Val missense_variant 0.22
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.25
ribD 2987612 c.774C>T synonymous_variant 0.1
thyA 3074252 p.Glu74* stop_gained 0.18
ald 3086638 c.-182G>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087179 c.360C>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641650 p.Trp39Leu missense_variant 0.15
alr 3841506 c.-86A>C upstream_gene_variant 0.21
rpoA 3877949 p.Thr187Pro missense_variant 1.0
clpC1 4040024 c.681A>G synonymous_variant 0.2
embA 4242406 c.-827A>C upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242788 p.Gly976Cys missense_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248095 p.Leu528Ile missense_variant 0.11
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249475 p.Trp988Arg missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269313 p.Lys174Thr missense_variant 1.0
ethA 4326104 p.Leu457Pro missense_variant 0.2
ethA 4326124 c.1350T>C synonymous_variant 0.17
ethA 4326239 p.Asn412Ser missense_variant 0.14
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