TB-Profiler result

Run: ERR4797128
Summary

Run ID: ERR4797128

Sample name:

Date: 01-04-2023 07:23:13

Number of reads: 3900833

Percentage reads mapped: 99.5

Strain: lineage2.2.1;lineage1.1.2

Drug-resistance: Other

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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 0.25
lineage1 Indo-Oceanic EAI RD239 0.77
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.74
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.27
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.77
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.2
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
gid 4407851 c.351delG frameshift_variant 0.75 streptomycin
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 0.75
gyrB 6124 c.885C>T synonymous_variant 0.77
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.8
gyrA 9143 c.1842T>C synonymous_variant 0.7
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.16
mshA 576108 p.Ala254Gly missense_variant 0.23
mshA 576482 p.Val379Leu missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 0.23
rpoB 760490 c.684C>T synonymous_variant 0.73
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.69
rpoC 763886 c.517C>A synonymous_variant 0.72
rpoC 765171 p.Pro601Leu missense_variant 0.77
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.18
mmpL5 776395 p.Phe696Leu missense_variant 0.72
mmpS5 779615 c.-710C>G upstream_gene_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801159 c.351C>T synonymous_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24
embR 1417019 p.Cys110Tyr missense_variant 0.74
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473067 n.1222C>T non_coding_transcript_exon_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167669 p.Phe982Val missense_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.73
PPE35 2168845 p.Thr590Ala missense_variant 0.32
Rv1979c 2222308 p.Asp286Gly missense_variant 0.66
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.8
eis 2715016 p.Arg106His missense_variant 0.7
ahpC 2726051 c.-142G>A upstream_gene_variant 0.69
pepQ 2860398 c.21A>C synonymous_variant 0.81
Rv2752c 3064632 c.1560C>T synonymous_variant 0.73
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087128 c.309C>T synonymous_variant 0.75
fbiD 3339734 p.Ala206Gly missense_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 0.75
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.89
fprA 3475159 p.Asn385Asp missense_variant 0.89
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
rpoA 3878630 c.-123G>C upstream_gene_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 0.8
embC 4240671 p.Thr270Ile missense_variant 0.84
embC 4241042 p.Asn394Asp missense_variant 0.77
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243194 c.-39C>T upstream_gene_variant 0.7
embA 4243460 c.228C>T synonymous_variant 0.22
embA 4243848 p.Val206Met missense_variant 0.74
embA 4245969 p.Pro913Ser missense_variant 0.83
embB 4246555 c.42G>C synonymous_variant 0.15
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4246567 c.54G>T synonymous_variant 0.12
embB 4246584 p.Arg24Pro missense_variant 0.14
embB 4247646 p.Glu378Ala missense_variant 0.78
aftB 4267647 p.Asp397Gly missense_variant 0.28
aftB 4268619 p.Val73Gly missense_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 0.88
aftB 4269606 c.-770T>C upstream_gene_variant 0.79
whiB6 4338473 p.Arg17Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.78
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.76
gid 4407927 p.Glu92Asp missense_variant 0.14