TB-Profiler result

Run: SRR12199460
Summary

Run ID: SRR12199460

Sample name:

Date: 03-04-2023 06:41:52

Number of reads: 443295

Percentage reads mapped: 99.32

Strain: lineage2.2.1.1

Drug-resistance: HR-TB

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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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.95
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrA 6988 c.-314C>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8230 p.Val310Asp missense_variant 0.22
gyrA 8288 c.989delA frameshift_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575409 p.Gly21Asp missense_variant 0.22
mshA 575646 p.Val100Glu missense_variant 0.18
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762897 p.Val1031Met missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764859 c.1491delG frameshift_variant 0.11
rpoC 767021 p.Asp1218Tyr missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.33
mmpL5 776021 c.2460G>C synonymous_variant 0.3
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778104 p.Leu126Trp missense_variant 0.11
mmpL5 778156 p.Tyr109His missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779619 c.-714A>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471829 n.-16delA upstream_gene_variant 0.17
rrl 1473832 n.178delG non_coding_transcript_exon_variant 0.67
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.22
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.5
rrl 1474553 n.896T>C non_coding_transcript_exon_variant 1.0
rrl 1475202 n.1545G>T non_coding_transcript_exon_variant 0.2
rrl 1475905 n.2248G>A non_coding_transcript_exon_variant 0.17
fabG1 1673981 p.Val181Ala missense_variant 0.4
inhA 1674427 p.Gly76Ser missense_variant 0.22
rpsA 1833351 c.-190delC upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102289 p.Val252Ile missense_variant 0.25
ndh 2102949 p.Lys32Glu missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.23
PPE35 2167868 c.2745A>C synonymous_variant 0.33
PPE35 2169125 p.Val496Ile missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.77
PPE35 2170053 p.Thr187Ser missense_variant 0.75
PPE35 2170201 p.Ala138Thr missense_variant 0.11
PPE35 2170278 p.Ala112Asp missense_variant 0.2
PPE35 2170385 c.228G>T synonymous_variant 0.18
PPE35 2170392 p.Gly74Ala missense_variant 0.18
Rv1979c 2221868 p.Asp433Asn missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519116 c.1002C>T synonymous_variant 0.12
eis 2714846 p.Val163Ile missense_variant 1.0
folC 2746332 p.Glu423* stop_gained 0.14
Rv2752c 3064677 p.Glu505Asp missense_variant 0.25
Rv2752c 3064816 p.Asp459Gly missense_variant 0.4
Rv2752c 3065229 c.963G>T synonymous_variant 0.14
thyA 3073912 p.Met187Thr missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448635 c.132C>T synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475360 c.1354C>A synonymous_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613243 c.-127C>T upstream_gene_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.19
clpC1 4039018 p.Ser563Ala missense_variant 0.11
clpC1 4039022 c.1683A>G synonymous_variant 0.12
panD 4044452 c.-171C>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248879 p.Thr789Met missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327309 c.-240G>C upstream_gene_variant 0.12
ethR 4327312 c.-237G>A upstream_gene_variant 0.12
ethA 4327317 p.Ile53Val missense_variant 0.12
ethR 4327321 c.-228G>C upstream_gene_variant 0.12
ethR 4327324 c.-225A>G upstream_gene_variant 0.12
ethR 4327327 c.-222A>G upstream_gene_variant 0.12
ethR 4327336 c.-213A>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0