TB-Profiler result

Run: SRR6964485
Summary

Run ID: SRR6964485

Sample name:

Date: 04-04-2023 18:14:17

Number of reads: 4277957

Percentage reads mapped: 99.35

Strain: lineage3;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 0.72
lineage1 Indo-Oceanic EAI RD239 0.28
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.27
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.32
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 0.22
gyrB 6124 c.885C>T synonymous_variant 0.21
gyrA 7290 c.-12A>G upstream_gene_variant 0.7
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.33
gyrA 8694 c.1393C>T synonymous_variant 0.62
gyrA 9143 c.1842T>C synonymous_variant 0.27
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.65
rpoB 760490 c.684C>T synonymous_variant 0.39
rpoC 762434 c.-936T>G upstream_gene_variant 0.75
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.38
rpoC 763886 c.517C>A synonymous_variant 0.38
rpoC 765171 p.Pro601Leu missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.17
mmpR5 779000 p.Asn4Thr missense_variant 0.72
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
fbiC 1303051 p.Val41Met missense_variant 0.23
embR 1417019 p.Cys110Tyr missense_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473609 n.-49G>C upstream_gene_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.37
Rv1979c 2222308 p.Asp286Gly missense_variant 0.26
Rv1979c 2223136 p.Ala10Val missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.76
pncA 2289365 c.-125delC upstream_gene_variant 0.7
kasA 2518132 c.18C>T synonymous_variant 0.19
ahpC 2726051 c.-142G>A upstream_gene_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 0.69
Rv2752c 3064632 c.1560C>T synonymous_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.37
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.33
fprA 3475159 p.Asn385Asp missense_variant 0.32
clpC1 4040517 p.Val63Ala missense_variant 0.3
embC 4240671 p.Thr270Ile missense_variant 0.25
embC 4241042 p.Asn394Asp missense_variant 0.24
embC 4242075 p.Arg738Gln missense_variant 0.64
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.28
embA 4244167 p.Ala312Val missense_variant 0.31
embA 4245957 p.Gly909Arg missense_variant 0.22
embA 4245969 p.Pro913Ser missense_variant 0.24
embB 4247646 p.Glu378Ala missense_variant 0.27
embB 4248631 c.2118G>A synonymous_variant 0.32
ubiA 4269387 p.Glu149Asp missense_variant 0.24
aftB 4269606 c.-770T>C upstream_gene_variant 0.25
ethA 4326432 p.Leu348Phe missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.32
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.25