TB-Profiler result

Run: SRR19415531
Summary

Run ID: SRR19415531

Sample name:

Date: 03-04-2023 21:37:30

Number of reads: 1399106

Percentage reads mapped: 99.51

Strain: lineage4;lineage3.1.1;lineage2.2.1;lineage1.1.2

Drug-resistance: Sensitive

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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
lineage3 East-African-Indian CAS RD750 0.18
lineage2 East-Asian Beijing RD105 0.13
lineage4 Euro-American LAM;T;S;X;H None 0.11
lineage1 Indo-Oceanic EAI RD239 0.63
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.59
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.16
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.12
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.56
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.15
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.1
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
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 0.56
gyrB 6124 c.885C>T synonymous_variant 0.51
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.72
gyrA 9143 c.1842T>C synonymous_variant 0.64
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.88
rpoB 759746 c.-61C>T upstream_gene_variant 0.15
rpoC 762434 c.-936T>G upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.88
rpoC 763884 p.Ala172Val missense_variant 0.66
rpoC 763886 c.517C>A synonymous_variant 0.66
rpoC 765171 p.Pro601Leu missense_variant 0.56
rpoC 767094 p.Ser1242Asn missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.9
mmpL5 776182 p.Asp767Asn missense_variant 0.15
mmpL5 779331 c.-851C>T upstream_gene_variant 0.59
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.65
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673283 c.-157A>C upstream_gene_variant 0.69
tlyA 1917777 c.-163A>G upstream_gene_variant 0.57
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.93
katG 2155557 c.555C>T synonymous_variant 0.59
PPE35 2167926 p.Leu896Ser missense_variant 0.83
PPE35 2167983 p.Gly877Asp missense_variant 0.51
PPE35 2170461 p.Gly51Glu missense_variant 0.22
Rv1979c 2221783 p.Ala461Glu missense_variant 0.67
Rv1979c 2222308 p.Asp286Gly missense_variant 0.54
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.12
pncA 2289365 c.-125delC upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 0.57
eis 2714526 c.805_806delAC frameshift_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 0.57
ahpC 2726105 c.-88G>A upstream_gene_variant 0.21
ahpC 2726672 c.480G>A synonymous_variant 0.55
Rv2752c 3064532 p.Thr554Ala missense_variant 0.56
Rv2752c 3064632 c.1560C>T synonymous_variant 0.51
Rv2752c 3064674 c.1518C>T synonymous_variant 0.55
Rv2752c 3065711 p.Gly161Ser missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.55
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.55
fprA 3475159 p.Asn385Asp missense_variant 0.6
clpC1 4040517 p.Val63Ala missense_variant 0.6
embC 4240671 p.Thr270Ile missense_variant 0.62
embC 4241042 p.Asn394Asp missense_variant 0.69
embC 4241562 p.Arg567His missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.18
embA 4243848 p.Val206Met missense_variant 0.62
embA 4245166 p.Pro645Gln missense_variant 0.52
embA 4245969 p.Pro913Ser missense_variant 0.56
embB 4247646 p.Glu378Ala missense_variant 0.5
aftB 4267300 p.Pro513Ser missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 0.68
aftB 4269606 c.-770T>C upstream_gene_variant 0.66
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.51
gid 4407588 c.615A>G synonymous_variant 0.91
gid 4407873 c.330G>T synonymous_variant 0.74
gid 4407927 p.Glu92Asp missense_variant 0.16