TB-Profiler result

Run: SRR6046420

Summary

Run ID: SRR6046420

Sample name:

Date: 04-04-2023 12:16:19

Number of reads: 258579

Percentage reads mapped: 89.29

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.5 streptomycin
ethA 4327147 p.Trp109* stop_gained 0.12 ethionamide
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766811 p.Ser1148Pro missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777573 p.Phe303Cys missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801396 c.588T>C synonymous_variant 0.25
fbiC 1303138 p.Leu70Ile missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471736 n.-110T>C upstream_gene_variant 0.2
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.67
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.4
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.4
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.4
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.4
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.6
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.4
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.4
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.4
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.6
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.4
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.67
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.67
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.5
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.4
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.4
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.4
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.4
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.8
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.67
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.33
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.33
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.33
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.4
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.4
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.4
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.33
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.33
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.62
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.71
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.71
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.67
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.8
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.8
inhA 1674738 c.539delG frameshift_variant 0.29
tlyA 1917886 c.-54C>A upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154471 c.1641T>C synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3068021 c.-76C>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087583 p.Val255Ala missense_variant 0.17
fprA 3473820 c.-187C>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987296 c.453C>T synonymous_variant 0.25
clpC1 4039633 p.Ile358Val missense_variant 0.21
embC 4240009 c.147G>A synonymous_variant 1.0
embC 4240179 p.Leu106Trp missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247686 p.Leu391Phe missense_variant 0.29
embB 4249506 p.Gln998Arg missense_variant 1.0
ethA 4326429 p.Phe349Ile missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0