TB-Profiler result

Run: ERR4815228
Summary

Run ID: ERR4815228

Sample name:

Date: 01-04-2023 13:44:49

Number of reads: 1110447

Percentage reads mapped: 98.97

Strain: lineage4.4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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 0.62 streptomycin
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
rpoB 759901 p.Arg32Gln missense_variant 0.22
rpoB 759910 p.Phe35Tyr missense_variant 0.15
rpoC 763376 p.Asp3Asn missense_variant 0.11
rpoC 765228 p.Met620Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776092 p.Ser797Gly missense_variant 1.0
mmpL5 778480 c.1A>G start_lost 0.15
mmpR5 779056 p.Met23Leu missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471775 n.-71G>A upstream_gene_variant 0.17
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.67
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.67
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.67
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.25
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.25
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.62
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.62
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.62
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
inhA 1674227 p.Arg9Leu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2153954 p.Phe720Leu missense_variant 0.12
katG 2155450 p.Ala221Val missense_variant 0.12
katG 2155619 p.Ile165Val missense_variant 0.12
PPE35 2168630 c.1983C>T synonymous_variant 0.18
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170001 c.612C>A synonymous_variant 0.11
Rv1979c 2222880 c.284dupG frameshift_variant 1.0
Rv1979c 2223262 c.-98C>G upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289007 p.Ala79Thr missense_variant 0.14
folC 2746350 c.1249C>T synonymous_variant 0.1
folC 2747643 c.-45G>A upstream_gene_variant 0.12
pepQ 2860436 c.-18C>T upstream_gene_variant 1.0
Rv2752c 3065348 p.Ala282Thr missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448417 c.-87C>T upstream_gene_variant 0.12
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612601 c.516C>T synonymous_variant 0.11
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3642764 c.1230C>T synonymous_variant 0.13
alr 3840549 c.871delG frameshift_variant 0.1
rpoA 3877702 c.805delG frameshift_variant 0.12
clpC1 4039908 p.Glu266Val missense_variant 0.14
panD 4043901 c.380delA frameshift_variant 0.18
embC 4241925 p.Arg688Leu missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326219 p.Val419Ile missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338621 c.-100G>T upstream_gene_variant 0.11
gid 4407804 p.Ala133Gly missense_variant 1.0