TB-Profiler result

Run: ERR8665510
Summary

Run ID: ERR8665510

Sample name:

Date: 02-04-2023 07:30:12

Number of reads: 211257

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 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
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 6665 p.Gln476Lys missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9326 c.2025G>T synonymous_variant 0.33
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 766190 p.Gly941Cys missense_variant 0.25
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 776357 p.Phe708Leu missense_variant 0.29
mmpL5 777902 c.579C>A synonymous_variant 0.4
mmpL5 778400 p.Met27Ile missense_variant 0.67
mmpL5 778431 p.Arg17Met missense_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779651 c.-746G>T upstream_gene_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800906 p.Pro33His missense_variant 0.4
Rv1258c 1406263 p.Gly360Cys missense_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406789 c.552C>A synonymous_variant 0.4
embR 1417186 c.162C>A synonymous_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472755 n.910G>T non_coding_transcript_exon_variant 0.2
rrs 1472950 n.1105C>A non_coding_transcript_exon_variant 0.22
rrl 1474108 n.451C>A non_coding_transcript_exon_variant 0.18
rrl 1474573 n.916C>A non_coding_transcript_exon_variant 0.17
rrl 1474874 n.1217A>G non_coding_transcript_exon_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834585 c.1044C>A synonymous_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103036 p.Pro3Thr missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154848 p.Pro422Thr missense_variant 0.6
katG 2156006 p.Gln36Lys missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169527 c.1086G>T synonymous_variant 0.5
PPE35 2170427 c.186G>A synonymous_variant 0.29
Rv1979c 2221893 c.1272C>A synonymous_variant 0.33
Rv1979c 2223162 c.3G>T synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289240 c.2T>C start_lost 1.0
eis 2714568 c.765C>A synonymous_variant 0.29
eis 2714599 p.Thr245Asn missense_variant 0.25
ribD 2987295 p.Arg153Ser missense_variant 0.29
Rv2752c 3065738 p.Asp152Tyr missense_variant 0.25
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
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640980 c.-555C>A upstream_gene_variant 0.29
fbiB 3642282 p.Glu250* stop_gained 0.33
rpoA 3878297 p.Glu71* stop_gained 0.25
ddn 3987026 c.183C>A synonymous_variant 0.18
ddn 3987070 p.Ala76Glu missense_variant 0.15
clpC1 4038707 c.1998C>A synonymous_variant 0.29
clpC1 4038760 p.Asp649Tyr missense_variant 0.5
clpC1 4039674 p.Pro344Gln missense_variant 0.4
panD 4044036 c.246G>T synonymous_variant 0.4
embC 4240436 p.Asp192Tyr missense_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
embA 4245152 c.1920C>A synonymous_variant 0.38
embA 4245155 c.1923C>A synonymous_variant 0.25
embB 4245779 c.-735C>A upstream_gene_variant 0.5
embB 4247323 c.810G>T synonymous_variant 0.5
embB 4249271 p.Asp920Tyr missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268344 p.Arg165Ser missense_variant 0.22
ethA 4327479 c.-6G>T upstream_gene_variant 0.17
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338404 p.Arg40Ser missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338676 c.-156delG upstream_gene_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0