TB-Profiler result

Run: ERR4831998
Summary

Run ID: ERR4831998

Sample name:

Date: 01-04-2023 21:15:31

Number of reads: 565358

Percentage reads mapped: 93.85

Strain: lineage2.2.1

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
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.Ser450Trp 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 2289043 p.Ser67Pro missense_variant 1.0 pyrazinamide
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
gyrA 9574 p.Arg758Pro missense_variant 0.12
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
rpoB 761909 p.Cys701Trp missense_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763348 c.-22C>A upstream_gene_variant 0.12
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 776740 p.Ile581Val missense_variant 0.1
mmpL5 777422 c.1059G>T synonymous_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305064 p.His712Asn missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416789 p.Ala187Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472465 n.620G>C non_coding_transcript_exon_variant 0.14
rrs 1472825 n.980G>T non_coding_transcript_exon_variant 0.15
rrl 1473908 n.251C>A non_coding_transcript_exon_variant 0.33
fabG1 1673347 c.-93C>A upstream_gene_variant 0.14
inhA 1674810 c.609C>T synonymous_variant 0.22
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
katG 2155377 c.735G>T synonymous_variant 0.14
PPE35 2167723 p.Thr964Ala missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168688 p.Pro642Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519144 p.Gly344Cys missense_variant 0.17
pepQ 2860299 c.120C>T synonymous_variant 0.11
ald 3086778 c.-42A>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087089 p.Ile90Met missense_variant 0.11
ald 3087536 c.717C>A synonymous_variant 0.13
ald 3087568 p.Val250Ala missense_variant 0.14
Rv3083 3448494 c.-10T>C upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475288 p.Ala428Ser missense_variant 0.2
Rv3236c 3612676 c.441A>G synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641452 p.Arg304Trp missense_variant 0.13
rpoA 3878368 p.Pro47Leu missense_variant 0.13
ddn 3986672 c.-172G>T upstream_gene_variant 0.15
ddn 3986700 c.-144C>A upstream_gene_variant 0.17
clpC1 4038729 p.Asn659Ser missense_variant 0.11
clpC1 4038833 p.Phe624Leu missense_variant 0.15
clpC1 4039706 p.Glu333Asp missense_variant 0.11
embC 4241863 p.Glu667Asp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242998 p.Ala1046Ser missense_variant 0.14
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243785 p.Leu185Met missense_variant 0.13
embA 4245991 p.Pro920Leu missense_variant 0.12
embB 4249647 p.Arg1045Gln missense_variant 0.29
aftB 4267436 c.1401G>T synonymous_variant 0.12
aftB 4267557 p.Ala427Val missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326126 p.Gly450Ser 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