TB-Profiler result

Run: ERR4797097
Summary

Run ID: ERR4797097

Sample name:

Date: 01-04-2023 07:21:46

Number of reads: 5161406

Percentage reads mapped: 99.6

Strain: lineage2.2.1;lineage1.1.2

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.81
lineage1 Indo-Oceanic EAI RD239 0.2
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.21
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.8
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.2
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.81
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 0.76 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.13 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.84 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.78 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 0.79 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.74 kanamycin
embB 4247429 p.Met306Val missense_variant 0.83 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 6112 p.Met291Ile missense_variant 0.2
gyrB 6124 c.885C>T synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.13
gyrA 8574 p.Leu425Phe missense_variant 0.23
gyrA 9047 c.1746C>T synonymous_variant 0.21
gyrA 9143 c.1842T>C synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 0.24
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.79
mshA 576000 p.Asp218Ala missense_variant 0.26
mshA 576108 p.Ala254Gly missense_variant 0.24
ccsA 620553 c.663T>C synonymous_variant 0.81
ccsA 620625 p.Ile245Met missense_variant 0.81
rpoB 760490 c.684C>T synonymous_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.13
rpoC 763886 c.517C>A synonymous_variant 0.15
rpoC 764817 p.Val483Ala missense_variant 0.86
rpoC 765171 p.Pro601Leu missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.71
mmpL5 776395 p.Phe696Leu missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.78
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.81
embR 1417019 p.Cys110Tyr missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rpsA 1834177 c.636A>C synonymous_variant 0.79
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.2
PPE35 2169369 p.Gly415Ala missense_variant 0.19
Rv1979c 2222308 p.Asp286Gly missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.28
ahpC 2726051 c.-142G>A upstream_gene_variant 0.22
ahpC 2726370 c.179dupT frameshift_variant 0.2
Rv2752c 3064632 c.1560C>T synonymous_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.27
Rv3083 3448714 p.Asp71His missense_variant 0.24
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.21
fprA 3475159 p.Asn385Asp missense_variant 0.26
Rv3236c 3612813 p.Thr102Ala missense_variant 0.72
rpoA 3878641 c.-134C>G upstream_gene_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.83
embA 4243848 p.Val206Met missense_variant 0.16
embA 4245969 p.Pro913Ser missense_variant 0.17
embB 4246584 p.Arg24Pro missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 0.16
embB 4249757 p.Thr1082Ala missense_variant 0.87
aftB 4267647 p.Asp397Gly missense_variant 0.83
aftB 4268619 p.Val73Gly missense_variant 0.2
aftB 4268765 c.72T>C synonymous_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 0.22
aftB 4269606 c.-770T>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.22
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.25
gid 4407927 p.Glu92Asp missense_variant 0.65