TB-Profiler result

Run: ERR4827440
Summary

Run ID: ERR4827440

Sample name:

Date: 01-04-2023 18:02:49

Number of reads: 759046

Percentage reads mapped: 99.44

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 0.99
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289027 p.Cys72Tyr missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val 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 6329 p.Glu364Gln missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8182 p.Gly294Asp missense_variant 0.2
gyrA 8981 c.1680G>T synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576089 c.750_769delTGATCGGCGCGCGGCCCGGG frameshift_variant 0.25
mshA 576111 p.Ala255Gly missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759887 c.81C>G synonymous_variant 0.12
rpoB 760231 p.Lys142Met missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763899 p.Leu177Pro missense_variant 0.18
rpoC 764925 p.Gly519Asp missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766930 p.Glu1187Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778871 p.Leu12Arg missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406392 c.949T>C synonymous_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473829 n.172G>A non_coding_transcript_exon_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
rpsA 1833392 c.-150C>A upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102102 p.Tyr314Phe missense_variant 0.13
ndh 2102809 p.Lys78Asn missense_variant 0.12
katG 2154543 c.1569G>A synonymous_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155661 p.Val151Leu missense_variant 0.11
katG 2155972 p.Val47Ala missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.56
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725962 c.-231C>T upstream_gene_variant 0.11
Rv2752c 3064880 p.Ile438Phe missense_variant 0.15
Rv2752c 3064991 p.Arg401Trp missense_variant 0.11
thyA 3073715 p.Pro253Ala missense_variant 1.0
thyA 3074177 c.294delG frameshift_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474223 p.Asp73His missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038405 p.Val767Ala missense_variant 0.11
embC 4241408 p.His516Asn missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245201 p.Thr657Ser missense_variant 0.14
embA 4245946 p.Ile905Thr missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.16
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4249086 p.Leu858Pro missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326533 p.Thr314Ile 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