TB-Profiler result

Run: ERR245663
Summary

Run ID: ERR245663

Sample name:

Date: 31-03-2023 18:13:37

Number of reads: 13641524

Percentage reads mapped: 99.36

Strain: lineage2.2.1

Drug-resistance: Other

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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
ethA 4327054 p.Tyr140* stop_gained 0.14 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 7493 c.192C>T synonymous_variant 0.26
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
ccsA 620748 c.858T>G synonymous_variant 0.26
rpoB 759831 p.Thr9Pro missense_variant 0.27
rpoC 762836 c.-534C>G upstream_gene_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.18
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 777399 p.Thr361Arg missense_variant 0.16
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406358 p.Ile328Thr missense_variant 0.21
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.17
rrl 1473911 n.254G>A non_coding_transcript_exon_variant 0.17
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.18
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.19
inhA 1674892 p.Asn231Asp missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.19
ndh 2103226 c.-184C>G upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715586 c.-254G>C upstream_gene_variant 0.3
folC 2746186 c.1413G>C synonymous_variant 0.22
pepQ 2859680 p.Leu247Val missense_variant 0.18
pepQ 2859974 p.Ala149Pro missense_variant 0.16
Rv2752c 3064741 p.Gly484Ala missense_variant 0.27
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448929 p.Tyr142* stop_gained 0.16
Rv3083 3449673 p.Tyr390* stop_gained 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.26
clpC1 4039932 p.Gly258Val missense_variant 0.29
embC 4241056 c.1194C>G synonymous_variant 0.23
embC 4242476 p.Pro872Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.28
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244375 c.1143C>G synonymous_variant 0.23
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.16
ethA 4327672 c.-199G>A upstream_gene_variant 0.21
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