TB-Profiler result

Run: ERR4815921
Summary

Run ID: ERR4815921

Sample name:

Date: 01-04-2023 14:08:32

Number of reads: 2257927

Percentage reads mapped: 98.51

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 0.38 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761786 c.1980C>T synonymous_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.15
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.15
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.22
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.22
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.3
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.3
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.3
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.3
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.3
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.27
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.27
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.36
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.58
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.46
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.46
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.38
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.36
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.31
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.31
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.31
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.31
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.31
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.31
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.31
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.38
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.38
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.4
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.4
rrs 1473017 n.1172A>T non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>T non_coding_transcript_exon_variant 0.12
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.67
rrl 1474658 n.1001A>G non_coding_transcript_exon_variant 0.6
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.6
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.5
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.5
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.5
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.43
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.5
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.4
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.5
rrl 1475713 n.2056C>T non_coding_transcript_exon_variant 0.2
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.22
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.17
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.17
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.17
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.17
rrl 1475772 n.2115A>C non_coding_transcript_exon_variant 0.17
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.15
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.2
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.19
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168863 c.1750C>T synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.14
Rv2752c 3067135 c.-944C>T upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241111 p.Val417Met missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407720 c.483C>G synonymous_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0