TB-Profiler result

Run: SRR12882439
Summary

Run ID: SRR12882439

Sample name:

Date: 03-04-2023 07:37:42

Number of reads: 2195072

Percentage reads mapped: 94.78

Strain: lineage1.2.1.2

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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.98
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
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 0.95
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491308 p.Ala176Thr missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763083 p.Arg1093Ser missense_variant 0.64
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777614 c.867C>T synonymous_variant 0.13
mmpL5 778318 p.Thr55Ala missense_variant 0.15
mmpR5 779347 p.Val120Met missense_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781802 c.243G>T synonymous_variant 0.12
Rv1258c 1406118 c.1222delC frameshift_variant 0.92
Rv1258c 1406498 p.Leu281Phe missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 0.95
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473273 n.1428G>C non_coding_transcript_exon_variant 0.14
rrs 1473314 n.1469A>C non_coding_transcript_exon_variant 0.38
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 1.0
rrl 1476520 n.2863G>A non_coding_transcript_exon_variant 0.12
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.14
inhA 1674793 p.Ala198Pro missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168300 c.2313C>T synonymous_variant 0.13
Rv1979c 2221894 p.Val424Gly missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519201 c.1088delG frameshift_variant 0.23
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726755 p.Gly188Ala missense_variant 0.35
ahpC 2726758 c.566_567insCG frameshift_variant 0.22
thyX 3067243 p.Leu235Met missense_variant 0.13
thyX 3067667 c.279G>A synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339232 p.Val39Leu missense_variant 0.14
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.99
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiA 3640366 c.-177G>T upstream_gene_variant 0.96
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.22
rpoA 3878599 c.-92C>G upstream_gene_variant 0.22
clpC1 4038936 p.Thr590Asn missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.95
clpC1 4040760 c.-56C>A upstream_gene_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embB 4245530 c.-984T>C upstream_gene_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.19
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246563 p.Leu17Trp missense_variant 0.23
embB 4246567 c.54G>T synonymous_variant 0.22
embB 4246866 p.Val118Gly missense_variant 0.21
embB 4246872 p.Ala120Val missense_variant 0.17
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.98
embB 4249329 p.Met939Thr missense_variant 0.11
aftB 4267881 p.Gly319Val missense_variant 0.3
aftB 4267894 p.Ile315Val missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269933 c.-100C>A upstream_gene_variant 0.14
whiB6 4338361 p.Arg54Gln missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.96
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408027 p.Leu59Arg missense_variant 0.97