TB-Profiler result

Run: ERR4831791
Summary

Run ID: ERR4831791

Sample name:

Date: 01-04-2023 21:07:30

Number of reads: 3470332

Percentage reads mapped: 99.53

Strain: lineage2.2.1;lineage1.1.1

Drug-resistance: HR-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 0.21
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.81
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.78
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.18
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
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid
folC 2747151 p.Ser150Gly missense_variant 0.78 para-aminosalicylic_acid
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 5627 p.Ala130Ser missense_variant 0.21
gyrB 6112 p.Met291Ile missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.26
gyrA 9143 c.1842T>C synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.77
ccsA 620625 p.Ile245Met missense_variant 0.74
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.26
rpoC 763886 c.517C>A synonymous_variant 0.27
rpoC 765171 p.Pro601Leu missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.84
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781694 c.135G>A synonymous_variant 0.21
Rv1258c 1406760 c.580_581insC frameshift_variant 0.84
embR 1417019 p.Cys110Tyr missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.23
inhA 1674109 c.-93C>T upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 0.76
rpsA 1834319 p.Val260Ile missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154575 p.Asp513Asn missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.22
PPE35 2169690 p.Gly308Asp missense_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 0.2
Rv1979c 2223144 p.Arg7Ser missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14
ahpC 2726763 p.Leu191Phe missense_variant 0.27
Rv2752c 3064632 c.1560C>T synonymous_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.16
fprA 3475159 p.Asn385Asp missense_variant 0.24
Rv3236c 3612813 p.Thr102Ala missense_variant 0.76
alr 3841612 c.-193_-192insC upstream_gene_variant 0.72
clpC1 4040517 p.Val63Ala missense_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 0.25
embC 4241042 p.Asn394Asp missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.73
embA 4243848 p.Val206Met missense_variant 0.21
embA 4244096 c.864C>T synonymous_variant 0.17
embA 4245969 p.Pro913Ser missense_variant 0.27
embB 4247646 p.Glu378Ala missense_variant 0.24
embB 4249622 p.Leu1037Ile missense_variant 0.27
aftB 4267647 p.Asp397Gly missense_variant 0.68
ubiA 4269387 p.Glu149Asp missense_variant 0.21
aftB 4269606 c.-770T>C upstream_gene_variant 0.19
ethA 4326337 p.Asn379Lys missense_variant 0.79
ethA 4328212 c.-740delC upstream_gene_variant 0.21
whiB6 4338242 p.Gln94Glu missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.16
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.22
gid 4407927 p.Glu92Asp missense_variant 0.82