TB-Profiler result

Run: SRR19428519
Summary

Run ID: SRR19428519

Sample name:

Date: 03-04-2023 21:38:51

Number of reads: 2314295

Percentage reads mapped: 99.3

Strain: lineage4.6.1.1

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
lineage4.6 Euro-American T;LAM None 0.09
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.62
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.28
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.12
lineage4.6.1.1 Euro-American T2-Uganda RD724 0.15
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
folC 2747144 p.Phe152Ser missense_variant 0.11 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 6112 p.Met291Ile missense_variant 0.6
gyrB 6124 c.885C>T synonymous_variant 0.61
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.65
gyrA 9143 c.1842T>C synonymous_variant 0.51
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.89
mshA 575634 p.Ala96Val missense_variant 0.18
mshA 576263 p.Leu306Met missense_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 0.26
rpoC 762434 c.-936T>G upstream_gene_variant 0.27
rpoC 763031 c.-339T>C upstream_gene_variant 0.8
rpoC 763884 p.Ala172Val missense_variant 0.69
rpoC 763886 c.517C>A synonymous_variant 0.8
rpoC 765171 p.Pro601Leu missense_variant 0.72
rpoC 765544 c.2175C>T synonymous_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 0.97
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 777384 p.Lys366Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407502 c.-162G>T upstream_gene_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 0.41
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673283 c.-157A>C upstream_gene_variant 0.68
inhA 1674916 p.Ala239Thr missense_variant 0.12
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 0.82
katG 2155557 c.555C>T synonymous_variant 0.58
PPE35 2167926 p.Leu896Ser missense_variant 0.8
PPE35 2167983 p.Gly877Asp missense_variant 0.61
Rv1979c 2221783 p.Ala461Glu missense_variant 0.61
Rv1979c 2222308 p.Asp286Gly missense_variant 0.58
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.28
pncA 2289365 c.-125delC upstream_gene_variant 0.28
kasA 2518132 c.18C>T synonymous_variant 0.56
ahpC 2726051 c.-142G>A upstream_gene_variant 0.81
ahpC 2726105 c.-88G>A upstream_gene_variant 0.26
ahpC 2726672 c.480G>A synonymous_variant 0.62
folC 2746825 c.774G>T synonymous_variant 0.11
Rv2752c 3064632 c.1560C>T synonymous_variant 0.59
Rv2752c 3064771 p.Ala474Val missense_variant 0.38
thyX 3067391 c.555G>T synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 0.84
ald 3087299 p.Met160Ile missense_variant 0.12
fbiD 3339050 c.-68C>A upstream_gene_variant 0.14
fbiD 3339510 c.393C>T synonymous_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 0.74
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.46
fprA 3475159 p.Asn385Asp missense_variant 0.73
fbiB 3641660 p.Asp42Glu missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.7
embC 4240172 p.Val104Met missense_variant 0.31
embC 4240671 p.Thr270Ile missense_variant 0.5
embC 4241562 p.Arg567His missense_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 0.25
embC 4242312 p.Gly817Val missense_variant 0.17
embA 4243661 c.429C>T synonymous_variant 0.17
embA 4243848 p.Val206Met missense_variant 0.78
embA 4245166 p.Pro645Gln missense_variant 0.65
embA 4245969 p.Pro913Ser missense_variant 0.56
embB 4247048 p.Pro179Ser missense_variant 1.0
embB 4249301 p.Arg930Ser missense_variant 0.17
embB 4249439 p.Glu976Lys missense_variant 0.17
aftB 4267610 c.1227C>T synonymous_variant 0.11
aftB 4268294 p.Cys181* stop_gained 0.14
ubiA 4269387 p.Glu149Asp missense_variant 0.63
aftB 4269606 c.-770T>C upstream_gene_variant 0.51
ubiA 4269713 p.Gly41Cys missense_variant 0.12
ethA 4328329 c.-856C>G upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.62
gid 4407588 c.615A>G synonymous_variant 0.81
gid 4407873 c.330G>T synonymous_variant 0.74
gid 4407950 p.Asp85Asn missense_variant 0.71