TB-Profiler result

Run: ERR2515631

Summary

Run ID: ERR2515631

Sample name:

Date: 31-03-2023 21:02:09

Number of reads: 358782

Percentage reads mapped: 99.7

Strain: lineage2.2.1

Drug-resistance: MDR-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 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
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpsL 781585 p.Arg9His missense_variant 0.17 streptomycin
katG 2154728 c.1383delG frameshift_variant 0.11 isoniazid
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 6400 c.-902C>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9027 c.1729dupT frameshift_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490934 p.Ala51Val missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576756 p.Arg470His missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764192 p.Glu275* stop_gained 0.15
rpoC 764223 p.Lys285Met missense_variant 0.11
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 777254 c.1227G>T synonymous_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801272 p.Ala155Val missense_variant 0.15
fbiC 1302737 c.-194C>A upstream_gene_variant 0.12
fbiC 1302911 c.-20T>C upstream_gene_variant 0.12
fbiC 1303511 c.582delT frameshift_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407380 c.-40C>A upstream_gene_variant 0.29
embR 1417273 c.75C>T synonymous_variant 0.11
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
tlyA 1918161 c.222G>C synonymous_variant 0.12
tlyA 1918641 c.702G>T synonymous_variant 0.11
ndh 2102665 c.377dupT frameshift_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167652 c.2960delC frameshift_variant 0.18
PPE35 2167824 p.Gly930Val missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168510 c.2103C>T synonymous_variant 0.15
PPE35 2170220 c.393C>T synonymous_variant 0.18
Rv1979c 2222656 p.Lys170Met missense_variant 0.11
Rv1979c 2222832 c.333T>C synonymous_variant 0.11
Rv1979c 2222934 c.231C>G synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290114 c.-874delC upstream_gene_variant 0.13
kasA 2518460 c.347delT frameshift_variant 0.17
kasA 2518491 p.Tyr126Cys missense_variant 0.18
folC 2747714 c.-116G>A upstream_gene_variant 0.14
pepQ 2860307 p.Gly38Trp missense_variant 0.12
Rv2752c 3064660 p.Val511Ala missense_variant 0.1
Rv2752c 3066368 c.-177C>G upstream_gene_variant 0.12
thyA 3074198 p.Pro92Ser missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339372 c.255C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642747 c.1214delC frameshift_variant 0.11
ddn 3987291 p.Glu150Gln missense_variant 0.11
clpC1 4038511 p.Asp732Tyr missense_variant 0.18
embC 4239743 c.-120G>A upstream_gene_variant 0.11
embC 4240555 p.Met231Ile missense_variant 0.11
embC 4241996 p.Thr712Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243888 c.660delG frameshift_variant 0.12
embB 4247084 p.Asp191His missense_variant 0.1
embB 4247895 p.Pro461Gln missense_variant 0.12
embB 4249118 p.Asp869Asn missense_variant 0.18
embB 4249221 p.Ala903Asp missense_variant 0.14
embB 4249497 p.Pro995Leu missense_variant 0.17
aftB 4267084 p.His585Tyr missense_variant 0.15
aftB 4267288 p.His517Tyr missense_variant 0.12
aftB 4267398 p.Pro480Arg missense_variant 0.11
aftB 4267594 p.Ala415Thr missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268545 p.Leu98Ile missense_variant 0.4
aftB 4268787 p.Phe17Ser missense_variant 0.15
ubiA 4269856 c.-23G>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338684 c.-163C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0