TB-Profiler result

Run: SRR6257061
Summary

Run ID: SRR6257061

Sample name:

Date: 04-04-2023 13:24:53

Number of reads: 443699

Percentage reads mapped: 97.96

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
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288878 p.Gln122* stop_gained 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_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 6729 p.Leu497Pro missense_variant 0.12
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 491331 p.Lys183Asn missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575602 c.255G>A synonymous_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760250 p.Met148Ile missense_variant 0.15
rpoB 762154 p.Ile783Thr missense_variant 0.15
rpoB 762156 c.2350_2351insA frameshift_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775595 c.2886C>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775736 c.2745C>G synonymous_variant 0.13
mmpL5 775741 c.2740C>T synonymous_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.29
mmpL5 777122 c.1359C>T synonymous_variant 0.29
mmpL5 777128 c.1353A>G synonymous_variant 0.4
mmpS5 778770 p.Asp46Tyr missense_variant 0.2
mmpR5 779318 p.Ala110Glu missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304871 c.1941G>A synonymous_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416222 p.Phe376Leu missense_variant 0.17
embR 1416232 p.Cys372Gly missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475084 n.1427G>A non_coding_transcript_exon_variant 0.15
rrl 1475102 n.1445C>A non_coding_transcript_exon_variant 0.15
rrl 1475188 n.1531C>A non_coding_transcript_exon_variant 0.14
rrl 1475714 n.2057G>A non_coding_transcript_exon_variant 0.13
rrl 1476186 n.2529T>A non_coding_transcript_exon_variant 0.18
rrl 1476681 n.3024T>C non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.28
fabG1 1673349 c.-91G>C upstream_gene_variant 0.28
fabG1 1673357 c.-83G>A upstream_gene_variant 0.24
fabG1 1673359 c.-81T>C upstream_gene_variant 0.24
fabG1 1673361 c.-79C>G upstream_gene_variant 0.24
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
rpsA 1833476 c.-66T>C upstream_gene_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103216 c.-174G>A upstream_gene_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156315 c.-204T>C upstream_gene_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.16
PPE35 2167865 c.2748G>C synonymous_variant 0.23
PPE35 2167868 c.2745A>C synonymous_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167939 c.2673_2674insAC frameshift_variant 0.11
PPE35 2168231 c.2382T>C synonymous_variant 0.22
PPE35 2168234 c.2379G>T synonymous_variant 0.22
PPE35 2169278 c.1335T>C synonymous_variant 0.11
PPE35 2169281 c.1332T>G synonymous_variant 0.11
PPE35 2169302 p.Met437Phe missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.44
Rv1979c 2222112 c.1052dupT frameshift_variant 1.0
Rv1979c 2222848 p.Trp106Leu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518577 p.Gly155Ser missense_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.5
kasA 2519143 c.1029G>C synonymous_variant 0.5
eis 2714964 c.369C>T synonymous_variant 0.15
eis 2715248 p.Gly29Ser missense_variant 0.14
eis 2715276 c.57G>T synonymous_variant 0.15
eis 2715450 c.-118T>C upstream_gene_variant 0.2
eis 2715585 c.-253C>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.29
Rv2752c 3065200 p.Gly331Val missense_variant 0.13
Rv2752c 3066137 p.Thr19Ala missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339452 p.Val112Glu missense_variant 0.14
fbiD 3339694 p.Ala193Thr missense_variant 0.25
Rv3083 3449775 c.1272C>A synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474109 p.Ala35Thr missense_variant 0.2
fprA 3475360 p.Arg452Trp missense_variant 0.22
Rv3236c 3612687 p.Gly144Ser missense_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613168 c.-52A>G upstream_gene_variant 0.13
fbiA 3640367 c.-176A>G upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.27
rpoA 3878483 p.Leu9Met missense_variant 0.2
ddn 3986931 p.Arg30Ser missense_variant 1.0
clpC1 4039642 p.Thr355Ser missense_variant 0.14
clpC1 4039829 p.Leu292Phe missense_variant 0.12
panD 4044320 c.-39C>T upstream_gene_variant 0.2
embC 4239863 c.1A>T initiator_codon_variant 0.25
embC 4240757 p.Thr299Gly missense_variant 0.2
embC 4241275 c.1413A>G synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243063 p.Tyr1067* stop_gained 0.4
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244457 p.Ala409Thr missense_variant 0.25
embA 4244832 p.Val534Met missense_variant 0.25
embA 4245950 p.Gln906His missense_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4247395 c.882C>T synonymous_variant 0.12
embB 4247512 c.999T>C synonymous_variant 0.18
embB 4247516 p.Asn335Asp missense_variant 0.18
embB 4247695 c.1182G>C synonymous_variant 0.22
embB 4247699 p.Met396Leu missense_variant 0.22
embB 4247986 c.1473C>T synonymous_variant 0.17
embB 4248019 c.1506G>T synonymous_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267831 p.Gly336Cys missense_variant 0.4
ethA 4326437 p.Leu346Pro missense_variant 0.15
ethA 4328302 c.-829C>A upstream_gene_variant 0.22
whiB6 4338214 c.306_307dupCG frameshift_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