TB-Profiler result

Run: ERR4818849

Summary

Run ID: ERR4818849

Sample name:

Date: 01-04-2023 15:47:16

Number of reads: 857134

Percentage reads mapped: 99.42

Strain: lineage3

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 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8140 p.His280Arg missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491286 c.504G>T synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.28
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759818 c.12C>T synonymous_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763154 p.Lys1116Asn missense_variant 0.12
rpoC 766297 c.2928G>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777013 c.1460_1467delCGGACGGC frameshift_variant 0.1
mmpL5 777186 p.Ala432Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472040 n.195T>A non_coding_transcript_exon_variant 0.15
rrl 1473707 n.50T>A non_coding_transcript_exon_variant 0.4
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.4
rpsA 1833361 c.-181G>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168150 c.2463T>C synonymous_variant 0.18
PPE35 2170193 p.Tyr140* stop_gained 0.22
PPE35 2170297 p.Gln106* stop_gained 0.2
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
pncA 2289651 c.-410T>C upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3068155 c.-210G>T upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642705 p.Arg391Cys missense_variant 0.11
alr 3840606 c.814delG frameshift_variant 0.12
alr 3841111 p.Gly104Cys missense_variant 0.11
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878446 p.Phe21Tyr missense_variant 0.11
rpoA 3878466 c.41delT frameshift_variant 0.12
embC 4240480 c.618G>T synonymous_variant 0.1
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244129 c.897G>A synonymous_variant 0.11
ethA 4328040 c.-567G>C upstream_gene_variant 1.0
whiB6 4338489 c.33C>A synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0