TB-Profiler result

Run: ERR8665507
Summary

Run ID: ERR8665507

Sample name:

Date: 02-04-2023 07:30:07

Number of reads: 214499

Percentage reads mapped: 99.56

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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
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
rpoC 764841 p.Ile491Thr 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
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326087 c.1386delA frameshift_variant 1.0 ethionamide, 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
gyrB 5234 c.-6C>A upstream_gene_variant 0.18
gyrB 5511 p.Ser91Tyr missense_variant 0.43
gyrB 5888 p.Glu217* stop_gained 0.29
gyrB 6824 p.Leu529Met missense_variant 0.22
gyrA 7573 p.Ser91* stop_gained 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8011 p.Ser237Tyr missense_variant 0.2
gyrA 8013 p.Gln238Lys missense_variant 0.18
gyrA 8200 p.Ser300Tyr missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9618 p.Glu773Gln missense_variant 0.29
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
rpoB 760490 c.684C>A synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763654 c.285C>A synonymous_variant 0.4
rpoC 766723 c.3354G>A 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 776704 p.Asp593Tyr missense_variant 0.33
mmpL5 777211 p.Asp424Tyr missense_variant 0.2
mmpS5 779489 c.-584C>A upstream_gene_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800747 c.-62C>A upstream_gene_variant 0.17
fbiC 1305070 p.Asp714Tyr missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471866 n.21C>A non_coding_transcript_exon_variant 0.5
rrs 1473173 n.1328C>A non_coding_transcript_exon_variant 0.25
rrl 1473514 n.-144C>A upstream_gene_variant 0.25
rrl 1475214 n.1557G>T non_coding_transcript_exon_variant 0.25
rrl 1475450 n.1793C>A non_coding_transcript_exon_variant 0.25
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.25
rpsA 1833409 c.-133C>A upstream_gene_variant 0.4
rpsA 1834093 c.552G>T synonymous_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918402 p.Leu155Met missense_variant 0.5
ndh 2103065 c.-23G>T upstream_gene_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156006 p.Gln36Lys missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221731 c.1434G>T synonymous_variant 0.25
Rv1979c 2222328 c.837G>T synonymous_variant 0.29
Rv1979c 2222420 p.Asp249Tyr missense_variant 0.5
Rv1979c 2223045 c.120C>A synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288898 p.Pro115Gln missense_variant 0.29
pncA 2289240 c.2T>C start_lost 1.0
kasA 2518610 p.Thr166Ala missense_variant 1.0
eis 2715087 c.246C>A synonymous_variant 0.67
ahpC 2726171 c.-22C>A upstream_gene_variant 0.2
ahpC 2726256 p.Asp22Tyr missense_variant 0.22
folC 2747420 p.Pro60His missense_variant 0.4
Rv2752c 3066308 c.-117G>T upstream_gene_variant 0.29
thyA 3074356 p.Ser39* stop_gained 0.33
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086846 c.32delA frameshift_variant 1.0
ald 3087076 p.Arg86Leu missense_variant 0.4
ald 3087348 p.Gly177Ser missense_variant 0.29
ald 3087723 p.Pro302Thr missense_variant 0.17
fbiD 3338940 c.-178C>A upstream_gene_variant 0.22
Rv3083 3449865 p.Gln454His missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474720 c.714G>T synonymous_variant 0.33
Rv3236c 3612471 p.Glu216* stop_gained 0.5
Rv3236c 3612477 p.Asp214Tyr missense_variant 0.5
Rv3236c 3612793 c.324C>A synonymous_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641960 c.426C>A synonymous_variant 0.67
alr 3840626 c.795C>A synonymous_variant 0.25
clpC1 4038555 p.Ile717Asn missense_variant 0.29
clpC1 4038832 p.Asp625Tyr missense_variant 0.29
clpC1 4039883 p.Lys274Asn missense_variant 0.4
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 4245794 c.-720G>T upstream_gene_variant 0.25
embB 4248109 c.1596C>A synonymous_variant 0.33
embB 4249201 p.Gln896His missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327359 p.Glu39* stop_gained 0.33
ethA 4328245 c.-772C>A upstream_gene_variant 0.4
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338558 c.-37G>T upstream_gene_variant 0.22
whiB6 4338592 c.-71G>T upstream_gene_variant 0.25
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