TB-Profiler result

Run: SRR6207274
Summary

Run ID: SRR6207274

Sample name:

Date: 02-08-2023 15:03:09

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 0.17 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
gyrB 6076 c.837C>T synonymous_variant 0.17
gyrB 6140 p.Val301Leu missense_variant 0.8
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 759983 c.177C>T synonymous_variant 0.22
rpoB 762660 p.Arg952Trp missense_variant 0.2
rpoB 762664 p.Leu953Arg missense_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765763 c.2399_2401delTCA disruptive_inframe_deletion 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778318 p.Thr55Ala missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406602 p.Phe247Leu missense_variant 0.22
atpE 1460856 c.-189C>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.17
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.2
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.16
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.13
rrl 1473661 n.4T>A non_coding_transcript_exon_variant 0.15
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.18
inhA 1673859 c.-343G>A upstream_gene_variant 0.33
inhA 1674410 p.His70Arg missense_variant 0.12
rpsA 1833856 c.315A>G synonymous_variant 0.22
rpsA 1833862 c.321G>C synonymous_variant 0.22
rpsA 1833874 c.333T>C synonymous_variant 0.22
rpsA 1833928 c.387G>C synonymous_variant 0.25
rpsA 1833940 c.399C>A synonymous_variant 0.25
rpsA 1833971 c.430C>T synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154666 c.1446G>C synonymous_variant 0.22
PPE35 2169351 p.Ala421Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289017 c.225T>C synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073988 c.483delT frameshift_variant 0.17
thyA 3074168 p.Pro102Ser missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087584 c.765C>A synonymous_variant 0.22
Rv3083 3449617 c.1116delC frameshift_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3642160 p.Leu209Pro missense_variant 0.13
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040644 c.61A>C synonymous_variant 0.13
clpC1 4040741 c.-37G>C upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247461 p.Met316Ile missense_variant 0.17
aftB 4267757 c.1080T>C synonymous_variant 0.33
ethR 4327345 c.-204G>A upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408366 c.-164C>T upstream_gene_variant 0.33