TB-Profiler result

Run: ERR2513440
Summary

Run ID: ERR2513440

Sample name:

Date: 31-03-2023 19:40:49

Number of reads: 793508

Percentage reads mapped: 83.07

Strain: lineage4.1.1.3

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 0.92 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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777308 c.1173C>T synonymous_variant 0.12
mmpL5 779307 c.-827T>C upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.38
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.68
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.68
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.74
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.75
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.76
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.76
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.79
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.78
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.64
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.64
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.38
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.79
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.79
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.8
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.84
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.91
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.93
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.93
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.8
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.75
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.4
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.78
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.78
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.87
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.84
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.9
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.9
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.92
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.92
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.78
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.59
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.46
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
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 1473049 n.1204T>G non_coding_transcript_exon_variant 0.5
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.5
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.67
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.67
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5
rrs 1473109 n.1264T>C non_coding_transcript_exon_variant 0.5
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.5
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5
rrs 1473112 n.1267A>G non_coding_transcript_exon_variant 0.5
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.4
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.4
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.33
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.29
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.6
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.67
rrl 1474774 n.1117A>G non_coding_transcript_exon_variant 0.67
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.67
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.5
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.25
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.29
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.2
PPE35 2168072 c.2541A>T synonymous_variant 0.11
Rv1979c 2222130 c.1035A>G synonymous_variant 1.0
Rv1979c 2222496 c.669G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715558 c.-226A>T upstream_gene_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.18
ribD 2987193 p.Ile119Val missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641113 c.575delA frameshift_variant 0.14
fbiB 3642772 p.Asp413Ala missense_variant 0.35
clpC1 4039567 p.Val380Met missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249662 p.Ala1050Gly missense_variant 0.12
aftB 4267634 c.1203G>T synonymous_variant 1.0
aftB 4269696 c.-860C>T upstream_gene_variant 1.0
gid 4407855 c.346_347dupCG frameshift_variant 0.1