TB-Profiler result

Run: ERR403282
Summary

Run ID: ERR403282

Sample name:

Date: 01-04-2023 04:23:07

Number of reads: 3817087

Percentage reads mapped: 99.62

Strain: lineage4.3.3;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 0.83
lineage4 Euro-American LAM;T;S;X;H None 0.18
lineage4.3 Euro-American (LAM) mainly-LAM None 0.21
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.81
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.81
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.19
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 0.47 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.88 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.18 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.57 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.19 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.79 isoniazid
pncA 2288887 p.Trp119Arg missense_variant 0.58 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.67 kanamycin
eis 2715369 c.-37G>T upstream_gene_variant 0.14 kanamycin
embB 4247429 p.Met306Val missense_variant 0.67 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.21 ethambutol
ethA 4326463 c.1010delT frameshift_variant 0.62 ethionamide, ethionamide
ethA 4327480 c.-7T>C upstream_gene_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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.83
mshA 575907 p.Ala187Val missense_variant 0.83
ccsA 620625 p.Ile245Met missense_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.73
rpoC 764995 c.1626C>G synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpL5 776182 p.Asp767Asn missense_variant 0.83
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.21
Rv1258c 1406760 c.580_581insC frameshift_variant 0.74
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.85
rpsA 1834836 p.Met432Thr missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.79
katG 2156196 c.-85C>T upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289226 p.Ile6Leu missense_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 0.17
ribD 2986827 c.-12G>A upstream_gene_variant 0.61
Rv2752c 3064895 p.Ala433Ser missense_variant 0.56
thyA 3073868 p.Thr202Ala missense_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 0.63
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 0.83
rpoA 3878641 c.-134C>G upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 0.18
clpC1 4038968 c.1737G>A synonymous_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.55
embA 4243460 c.228C>T synonymous_variant 0.83
aftB 4267647 p.Asp397Gly missense_variant 0.73
whiB6 4338371 p.Thr51Pro missense_variant 0.64
whiB6 4338563 c.-42G>T upstream_gene_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.83
gid 4407927 p.Glu92Asp missense_variant 0.84
gid 4408156 p.Leu16Arg missense_variant 0.18