TB-Profiler result

Run: ERR5866377
Summary

Run ID: ERR5866377

Sample name:

Date: 02-04-2023 00:39:17

Number of reads: 877184

Percentage reads mapped: 97.27

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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 0.97
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
gyrA 7582 p.Asp94Gly missense_variant 0.2 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.92 streptomycin
katG 2154045 p.Trp689* stop_gained 0.14 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 0.95 kanamycin, amikacin
embB 4247730 p.Gly406Ala missense_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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7757 p.Phe152Leu missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491481 c.700delT frameshift_variant 0.15
fgd1 491632 p.Trp284Arg missense_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 766627 c.3258G>T synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.93
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776745 p.Arg579Leu missense_variant 0.11
mmpL5 777010 c.1470delA frameshift_variant 0.11
mmpL5 777185 c.1296G>A synonymous_variant 0.11
mmpL5 777414 p.Ala356Val missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304021 p.His364Leu missense_variant 0.2
fbiC 1305037 p.Arg703Trp missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474453 n.796T>C non_coding_transcript_exon_variant 0.12
fabG1 1673378 c.-62C>T upstream_gene_variant 0.13
fabG1 1673602 p.Leu55Met missense_variant 0.2
fabG1 1673972 p.Ala178Glu missense_variant 0.17
inhA 1674305 c.106_108delCTG conservative_inframe_deletion 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918018 p.Ile27Val missense_variant 1.0
ndh 2102752 p.Gln97His missense_variant 0.12
ndh 2102974 c.69G>A synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.95
PPE35 2169797 c.816G>T synonymous_variant 0.13
Rv1979c 2223063 c.102A>G synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289071 p.His57Gln missense_variant 0.89
pncA 2290078 c.-837C>A upstream_gene_variant 0.29
kasA 2518600 c.486C>T synonymous_variant 0.17
kasA 2518601 p.Gly163Trp missense_variant 0.17
eis 2715058 p.Arg92His missense_variant 0.15
eis 2715332 p.Val1Leu missense_variant 0.94
eis 2715533 c.-201T>C upstream_gene_variant 0.12
ahpC 2726516 p.Phe108Leu missense_variant 0.12
folC 2746598 p.Thr334Ile missense_variant 0.18
Rv2752c 3064698 c.1494C>A synonymous_variant 0.18
Rv2752c 3065518 p.Leu225Pro missense_variant 1.0
Rv2752c 3066102 c.90C>T synonymous_variant 0.11
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449436 c.933G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475264 c.1259dupC frameshift_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641382 p.Cys280* stop_gained 0.18
fbiB 3641952 p.Leu140Val missense_variant 0.12
rpoA 3877969 p.Ala180Gly missense_variant 1.0
rpoA 3878119 c.388dupG frameshift_variant 0.12
ddn 3987235 p.Pro131Gln missense_variant 0.13
ddn 3987267 p.Arg142Ser missense_variant 0.15
panD 4043917 p.Ala122Glu missense_variant 0.14
embC 4240049 c.191delA frameshift_variant 0.33
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 4247666 p.Trp385Arg missense_variant 0.1
embB 4247987 p.Val492Met missense_variant 0.11
aftB 4267175 c.1662C>T synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268017 p.Val274Leu missense_variant 0.1
aftB 4268042 c.795A>G synonymous_variant 0.1
aftB 4268582 c.255C>T synonymous_variant 0.14
ubiA 4269943 c.-111delG upstream_gene_variant 0.15
ethA 4326155 p.Leu440Pro missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 0.92
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