TB-Profiler result

Run: ERR4818027
Summary

Run ID: ERR4818027

Sample name:

Date: 01-04-2023 15:19:39

Number of reads: 1306857

Percentage reads mapped: 97.45

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 0.82 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 8414 p.Asp371Glu missense_variant 0.1
gyrA 9791 c.2490C>A synonymous_variant 0.11
rpoB 760673 c.867G>T synonymous_variant 0.12
rpoC 763977 p.Arg203His missense_variant 0.12
rpoC 764581 p.Asp404Glu missense_variant 0.2
rpoC 765447 p.Gln693Arg missense_variant 0.11
mmpL5 775633 p.Gln950Lys missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777304 c.1176delC frameshift_variant 0.11
mmpL5 777649 p.Ala278Ser missense_variant 0.14
mmpS5 778547 p.Gly120Asp missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800851 p.Gln15Lys missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.6
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.6
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.6
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.8
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.83
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.82
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.82
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.88
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.88
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.77
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.62
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.56
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.83
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.81
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.81
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.73
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.7
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.15
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.73
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.84
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.84
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.11
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.78
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.11
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.72
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.77
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.67
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.5
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.45
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.58
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.57
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.54
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.54
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.54
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.54
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.57
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.57
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.57
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.36
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.27
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.3
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.3
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.3
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.27
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.17
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.33
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476052 n.2395A>G non_coding_transcript_exon_variant 0.5
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.4
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.4
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.4
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.57
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.57
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.57
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.43
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.47
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47
rrl 1476389 n.2732G>A non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.36
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36
inhA 1674852 c.651G>A synonymous_variant 1.0
tlyA 1917866 c.-74C>A upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167787 c.2826C>A synonymous_variant 0.13
PPE35 2168527 p.Gly696* stop_gained 0.11
PPE35 2169897 p.Ser239Phe missense_variant 0.14
Rv1979c 2223021 c.144G>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065362 p.Gly277Asp missense_variant 0.13
thyA 3074230 p.Asp81Gly missense_variant 1.0
Rv3236c 3612807 p.Gly104Ser missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
rpoA 3878454 c.54A>T synonymous_variant 0.12
clpC1 4038990 p.Gly572Val missense_variant 0.17
clpC1 4040206 p.Thr167Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0