TB-Profiler result

Run: ERR019562
Summary

Run ID: ERR019562

Sample name:

Date: 31-03-2023 07:57:12

Number of reads: 1982245

Percentage reads mapped: 94.93

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 0.99
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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761097 p.Ser431Gly missense_variant 1.0 rifampicin
rpoB 761141 p.His445Gln missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289008 c.233dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val 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 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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
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 777487 p.Phe332Val missense_variant 1.0
mmpR5 779243 p.Val85Gly missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781602 c.45_46dupGA frameshift_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416222 p.Phe376Leu missense_variant 0.13
embR 1416232 p.Cys372Gly missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154181 p.Gly644Asp missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156225 c.-114T>C upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.21
PPE35 2169866 c.747G>C synonymous_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715368 c.-54_-37delGTCGTCGTAATATTCACG upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.21
Rv2752c 3064552 p.Arg547Pro missense_variant 0.43
thyX 3067995 c.-50A>C upstream_gene_variant 0.44
thyA 3073806 c.666C>G synonymous_variant 0.21
thyA 3074230 p.Asp81Gly missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339153 p.Leu12Phe missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642772 p.Asp413Ala missense_variant 0.3
clpC1 4039932 p.Gly258Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.41
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.9
ubiA 4269529 p.Ala102Gly missense_variant 0.38
ubiA 4270005 c.-172C>G upstream_gene_variant 0.29
ethA 4326623 p.Pro284Leu 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