TB-Profiler result

Run: SRR19428620
Summary

Run ID: SRR19428620

Sample name:

Date: 03-04-2023 21:42:36

Number of reads: 1553202

Percentage reads mapped: 91.57

Strain: 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 0.09
lineage1 Indo-Oceanic EAI RD239 0.88
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.89
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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 0.97
gyrB 6124 c.885C>T synonymous_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.85
gyrA 9143 c.1842T>C synonymous_variant 0.9
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490688 c.-95G>T upstream_gene_variant 0.22
fgd1 491286 c.504G>T synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575606 p.Glu87* stop_gained 0.14
mshA 575792 p.Asp149Tyr missense_variant 0.25
mshA 575929 c.582C>A synonymous_variant 0.2
mshA 576204 p.Ala286Val missense_variant 0.18
mshA 576221 p.Gly292Trp missense_variant 0.17
mshA 576394 c.1047G>A synonymous_variant 0.15
mshA 576775 c.1428C>T synonymous_variant 0.17
rpoB 760490 c.684C>T synonymous_variant 0.93
rpoC 762434 c.-936T>G upstream_gene_variant 0.11
rpoC 762737 c.-633C>A upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.85
rpoC 763886 c.517C>A synonymous_variant 0.92
rpoC 765171 p.Pro601Leu missense_variant 0.85
rpoC 766430 p.Gly1021Cys missense_variant 0.15
rpoC 766942 c.3573C>A synonymous_variant 0.12
rpoC 766977 p.Gly1203Val missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.89
mmpR5 779303 p.Arg105His missense_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303051 p.Val41Met missense_variant 0.82
embR 1417019 p.Cys110Tyr missense_variant 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834847 p.Ala436Thr missense_variant 0.17
rpsA 1834874 p.Ala445Thr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102211 p.Ala278Ser missense_variant 0.25
ndh 2102245 c.798C>A synonymous_variant 0.29
ndh 2102292 p.Asp251Asn missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.9
PPE35 2170207 p.Ala136Thr missense_variant 0.2
PPE35 2170218 p.Ala132Glu missense_variant 0.2
PPE35 2170341 p.Gln91Arg missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 0.87
Rv1979c 2223136 p.Ala10Val missense_variant 0.95
Rv1979c 2223200 c.-36G>A upstream_gene_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 0.89
kasA 2518954 c.840C>A synonymous_variant 0.17
kasA 2518973 p.Ala287Ser missense_variant 0.17
eis 2715581 c.-249C>T upstream_gene_variant 0.4
ahpC 2726051 c.-142G>A upstream_gene_variant 0.86
folC 2746287 p.Asp438Tyr missense_variant 0.25
folC 2746354 p.Glu415Asp missense_variant 1.0
folC 2746726 p.Leu291Phe missense_variant 0.14
pepQ 2859595 p.Ala275Val missense_variant 0.14
pepQ 2859621 c.798G>T synonymous_variant 0.5
pepQ 2859643 p.Ala259Val missense_variant 0.33
pepQ 2860158 c.261C>A synonymous_variant 1.0
ribD 2987385 p.Ala183Ser missense_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087326 c.507C>A synonymous_variant 0.33
fbiD 3339360 c.243C>A synonymous_variant 0.15
Rv3083 3448714 p.Asp71His missense_variant 0.9
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.93
fprA 3475159 p.Asn385Asp missense_variant 0.74
fbiB 3641490 c.-45G>T upstream_gene_variant 0.2
fbiB 3641596 p.Pro21His missense_variant 0.17
fbiB 3642239 c.705G>T synonymous_variant 1.0
fbiB 3642287 c.753G>T synonymous_variant 1.0
clpC1 4038213 p.Asp831Gly missense_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 0.96
embC 4240597 c.735G>T synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240970 p.Ala370Thr missense_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 0.5
embC 4241075 p.Gly405Cys missense_variant 0.2
embC 4241093 p.Cys411Arg missense_variant 0.25
embC 4241562 p.Arg567His missense_variant 0.18
embC 4241704 c.1842C>A synonymous_variant 0.15
embC 4242273 p.Gly804Val missense_variant 0.22
embC 4242401 p.Arg847Ser missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242712 p.Gln950His missense_variant 0.29
embA 4242721 c.-512G>T upstream_gene_variant 0.29
embA 4243816 p.Phe195Ser missense_variant 0.17
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244167 p.Ala312Val missense_variant 0.78
embA 4245495 p.Gly755Ser missense_variant 0.22
embA 4245603 p.Gly791Arg missense_variant 0.2
embA 4245670 p.Ala813Asp missense_variant 0.17
embA 4245810 p.Pro860Ser missense_variant 0.13
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246760 p.Val83Met missense_variant 1.0
embB 4247027 p.Leu172Met missense_variant 0.22
embB 4247783 c.1270C>A synonymous_variant 0.22
aftB 4267934 c.903G>T synonymous_variant 0.2
aftB 4267991 c.846G>T synonymous_variant 0.13
aftB 4268618 c.219G>T synonymous_variant 0.2
aftB 4268876 c.-40G>A upstream_gene_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 0.8
aftB 4269606 c.-770T>C upstream_gene_variant 0.86
aftB 4269729 c.-893G>T upstream_gene_variant 0.13
ubiA 4269808 p.Pro9His missense_variant 0.14
ethA 4326432 p.Leu348Phe missense_variant 0.86
ethR 4328036 p.Pro163Leu missense_variant 0.25
whiB6 4338232 p.Ser97Tyr missense_variant 0.17
whiB6 4338289 p.Gly78Val missense_variant 0.25
whiB6 4338324 c.198C>A synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.88
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.92