TB-Profiler result

Run: SRR6855733
Summary

Run ID: SRR6855733

Sample name:

Date: 04-04-2023 17:43:53

Number of reads: 482715

Percentage reads mapped: 99.63

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 0.99
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 4327347 p.Gly43Cys missense_variant 0.15 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 5854 c.615C>T synonymous_variant 0.25
gyrA 6862 c.-440C>A upstream_gene_variant 0.15
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
mshA 576500 p.Ile385Leu missense_variant 0.15
ccsA 619907 p.Val6Ala missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761752 p.Ala649Val missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764934 p.Ile522Thr missense_variant 0.14
rpoC 765087 p.Pro573Leu missense_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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302835 c.-96C>T upstream_gene_variant 0.13
fbiC 1305499 c.2569T>C stop_lost&splice_region_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472672 n.830delT non_coding_transcript_exon_variant 0.12
rrl 1476525 n.2868A>T non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834978 c.1437C>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918713 c.774T>C synonymous_variant 0.13
ndh 2103185 c.-145_-144delGT upstream_gene_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156233 c.-122C>A upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289302 c.-61C>A upstream_gene_variant 0.15
eis 2714444 p.Arg297Cys missense_variant 0.14
eis 2714676 c.657T>C synonymous_variant 0.12
eis 2714728 p.Ala202Val missense_variant 0.11
eis 2715261 p.Phe24Leu missense_variant 0.11
ahpC 2726331 p.Trp47Arg missense_variant 0.14
folC 2747167 p.Lys144Asn missense_variant 1.0
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087616 p.Asp266Gly missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642256 p.Phe241Ser missense_variant 0.12
rpoA 3877970 p.Ala180Pro missense_variant 0.13
ddn 3986705 c.-138delA upstream_gene_variant 0.1
clpC1 4038692 p.Ser671* stop_gained 0.11
clpC1 4038702 p.Leu668Pro missense_variant 0.1
clpC1 4039771 p.Leu312Val missense_variant 0.12
clpC1 4040091 p.Ser205Tyr missense_variant 0.12
embC 4239664 c.-199C>T upstream_gene_variant 0.12
embC 4240306 c.446dupG frameshift_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245001 p.Phe590Ser missense_variant 0.14
embA 4245441 p.Asp737Asn missense_variant 0.17
embB 4246939 c.426C>T synonymous_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269513 c.320delT frameshift_variant 0.11
ubiA 4269830 p.Ser2Cys missense_variant 0.11
ethR 4327946 p.Glu133Gly missense_variant 0.14
ethA 4328013 c.-540G>A upstream_gene_variant 0.2
whiB6 4338377 p.Ala49Thr missense_variant 0.13
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