TB-Profiler result

Run: ERR5865299
Summary

Run ID: ERR5865299

Sample name:

Date: 01-04-2023 23:55:45

Number of reads: 2219743

Percentage reads mapped: 99.57

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 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile 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
gyrB 5892 p.Val218Asp missense_variant 0.12
gyrB 6626 p.Ala463Pro missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7810 c.513delC frameshift_variant 0.12
gyrA 9196 p.Val632Glu missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575167 c.-181G>A upstream_gene_variant 0.25
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760210 p.Asn135Ser missense_variant 0.11
rpoB 760337 c.535delG frameshift_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763641 p.Arg91Leu missense_variant 0.13
rpoC 764936 p.Gln523Lys missense_variant 1.0
rpoC 766120 c.2751A>G synonymous_variant 0.18
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 777033 c.1447delG frameshift_variant 0.12
mmpL5 777800 c.681C>A synonymous_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304204 p.Ala425Asp missense_variant 0.29
Rv1258c 1406323 p.Ala340Thr missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472291 n.446G>C non_coding_transcript_exon_variant 0.2
rrs 1472899 n.1055delG non_coding_transcript_exon_variant 0.22
rrs 1472931 n.1089delC non_coding_transcript_exon_variant 0.33
rrl 1475930 n.2273G>T non_coding_transcript_exon_variant 0.13
rrl 1476226 n.2569G>A non_coding_transcript_exon_variant 0.33
rrl 1476431 n.2774G>A non_coding_transcript_exon_variant 0.1
rrl 1476663 n.3006C>A non_coding_transcript_exon_variant 0.2
rpsA 1834032 p.Tyr164Phe missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834630 c.1090delC frameshift_variant 0.11
tlyA 1917769 c.-171C>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102861 p.Gly61Glu missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155168 p.Ser315Ala missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221822 p.Ser448* stop_gained 0.12
Rv1979c 2222167 p.Ser333Ile missense_variant 0.2
Rv1979c 2223025 p.Ala47Glu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289333 c.-93dupT upstream_gene_variant 0.11
eis 2714194 p.Ser380Tyr missense_variant 0.11
eis 2714296 p.Ala346Glu missense_variant 0.14
ahpC 2726748 p.Asp186Asn missense_variant 0.12
folC 2746197 p.Ile468Val missense_variant 0.11
folC 2746238 p.Pro454Gln missense_variant 0.12
folC 2747777 c.-179C>G upstream_gene_variant 0.11
pepQ 2859321 c.1098C>A synonymous_variant 0.13
pepQ 2860255 p.Ala55Asp missense_variant 0.13
ribD 2987242 p.Arg135Gln missense_variant 0.12
thyX 3067285 p.Ala221Thr missense_variant 0.15
thyA 3074490 c.-19G>T upstream_gene_variant 0.12
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087638 c.819C>A synonymous_variant 0.12
fbiD 3338961 c.-157G>A upstream_gene_variant 0.12
Rv3083 3448356 c.-148G>A upstream_gene_variant 0.18
fprA 3473821 c.-186C>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474788 c.785delC frameshift_variant 0.12
fprA 3475101 c.1095C>A synonymous_variant 0.12
Rv3236c 3612713 p.Arg135Gln missense_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640755 c.-780C>G upstream_gene_variant 0.17
fbiB 3642769 p.Leu412Arg missense_variant 0.14
alr 3841589 c.-169C>T upstream_gene_variant 0.11
ddn 3986822 c.-21delT upstream_gene_variant 0.11
ddn 3987029 c.186C>T synonymous_variant 0.17
clpC1 4039300 p.Arg469Ser missense_variant 0.25
panD 4044325 c.-44C>T upstream_gene_variant 0.11
embC 4240248 p.Asp129Gly missense_variant 0.11
embC 4242295 p.Asp811Glu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.11
embA 4243317 p.Gly29Asn missense_variant 0.14
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246726 c.213G>A synonymous_variant 1.0
embB 4247491 c.978G>T synonymous_variant 0.11
embB 4249112 p.Lys867Glu missense_variant 0.15
aftB 4267119 p.Ala573Val missense_variant 0.12
aftB 4267207 p.Val544Leu missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327648 p.Glu34* stop_gained 0.15
whiB6 4338371 p.Thr51Pro 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