TB-Profiler result

Run: ERR5863902
Summary

Run ID: ERR5863902

Sample name:

Date: 01-04-2023 22:59:05

Number of reads: 2098303

Percentage reads mapped: 99.6

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.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 2289009 p.Gly78Asp missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326770 c.703delT frameshift_variant 1.0 ethionamide, 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
gyrB 6119 p.Asn294Asp missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7432 p.Val44Glu missense_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.501delC frameshift_variant 0.11
gyrA 8292 p.Leu331Val missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9571 p.Arg757Leu missense_variant 0.11
fgd1 491283 c.506delG frameshift_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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766606 c.3238delA frameshift_variant 0.12
rpoC 767042 p.Ser1225Pro 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 776765 c.1716G>A synonymous_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475104 n.1450delG non_coding_transcript_exon_variant 0.25
rrl 1475275 n.1618C>A non_coding_transcript_exon_variant 0.11
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.13
rrl 1476047 n.2390G>C non_coding_transcript_exon_variant 0.25
rrl 1476704 n.3047G>A 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
ndh 2102417 p.Ala209Val missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168909 c.1704C>A synonymous_variant 0.12
Rv1979c 2222115 p.Met350Ile missense_variant 0.12
Rv1979c 2222239 c.925delC frameshift_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714853 c.480C>G synonymous_variant 0.1
eis 2714937 c.396G>A synonymous_variant 0.11
folC 2746467 p.Val378Leu missense_variant 0.12
Rv2752c 3064564 c.1627delG frameshift_variant 0.17
Rv2752c 3064944 c.1248G>T synonymous_variant 0.18
Rv2752c 3065761 p.Phe144Ser missense_variant 0.12
ald 3086731 c.-89A>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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246622 p.Gly37Cys missense_variant 0.12
embB 4246688 p.Pro59Thr missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327531 c.-58T>G upstream_gene_variant 0.1
whiB6 4338371 p.Thr51Pro 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
gid 4407947 p.Leu86Ile missense_variant 0.17