TB-Profiler result

Run: SRR19409781
Summary

Run ID: SRR19409781

Sample name:

Date: 03-04-2023 21:37:26

Number of reads: 1399021

Percentage reads mapped: 99.6

Strain: lineage4;lineage3.1.1;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 0.74
lineage4 Euro-American LAM;T;S;X;H None 0.1
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.1
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.61
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.13
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.63
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 0.15
gyrB 6124 c.885C>T synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.14
gyrA 9143 c.1842T>C synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.89
rpoB 759746 c.-61C>T upstream_gene_variant 0.56
rpoC 762434 c.-936T>G upstream_gene_variant 0.73
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 765171 p.Pro601Leu missense_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406349 p.Ile331Ser missense_variant 0.45
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.89
katG 2155557 c.555C>T synonymous_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 0.78
PPE35 2167983 p.Gly877Asp missense_variant 0.14
PPE35 2170461 p.Gly51Glu missense_variant 0.6
Rv1979c 2222308 p.Asp286Gly missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.5
pncA 2289365 c.-125delC upstream_gene_variant 0.84
eis 2714908 p.Val142Gly missense_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 0.87
ald 3086788 c.-32T>C upstream_gene_variant 0.93
Rv3083 3448714 p.Asp71His missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.13
fprA 3475159 p.Asn385Asp missense_variant 0.21
alr 3840636 p.Pro262Gln missense_variant 0.19
embC 4240172 p.Val104Met missense_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 0.15
embC 4241562 p.Arg567His missense_variant 0.64
embC 4242075 p.Arg738Gln missense_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243813 p.Arg194Gln missense_variant 0.13
embA 4243848 p.Val206Met missense_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 0.14
embB 4247646 p.Glu378Ala missense_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 0.12
ethA 4327629 c.-156C>T upstream_gene_variant 0.11
ethA 4328329 c.-856C>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407873 c.330G>T synonymous_variant 0.13