TB-Profiler result

Run: ERR4820622
Summary

Run ID: ERR4820622

Sample name:

Date: 01-04-2023 16:46:52

Number of reads: 697575

Percentage reads mapped: 83.54

Strain: lineage4.3.4.2

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
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 0.84 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 759620 c.-187A>C upstream_gene_variant 0.27
rpoC 762794 c.-576C>T upstream_gene_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777623 c.858G>A synonymous_variant 0.14
mmpL5 777626 c.855C>T synonymous_variant 0.14
mmpL5 778192 p.Gly97Ser missense_variant 0.18
mmpL5 778350 p.Ala44Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407275 c.66T>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.5
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.58
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.58
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.82
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.82
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.84
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.84
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.85
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.85
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.81
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.72
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.83
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.9
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.86
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.92
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.92
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.88
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.88
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.79
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.79
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.5
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.73
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.62
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.79
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.83
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.87
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.87
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.8
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.83
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.65
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.6
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.61
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.25
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.25
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.38
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.38
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.33
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.33
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.33
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.33
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.27
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.25
rrs 1473291 n.1446G>A non_coding_transcript_exon_variant 0.25
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.25
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.25
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.25
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.25
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.27
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.27
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.8
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.8
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.8
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.86
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.75
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.75
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.75
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.62
rrl 1476298 n.2641C>T non_coding_transcript_exon_variant 1.0
rrl 1476392 n.2735A>G non_coding_transcript_exon_variant 0.25
rpsA 1833790 c.249T>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.13
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2170066 p.Ala183Thr missense_variant 0.25
Rv1979c 2222185 c.979delT frameshift_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.27
folC 2746334 p.Gly422Ala missense_variant 0.11
folC 2746833 p.Val256Leu missense_variant 0.2
folC 2747006 p.Ser198Ile missense_variant 0.1
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449079 p.Leu192Phe missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612113 p.Glu335Gly missense_variant 0.17
rpoA 3878097 c.411G>A synonymous_variant 0.1
ddn 3986817 c.-27C>T upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243154 c.-79C>A upstream_gene_variant 0.15
embA 4243260 p.His10Tyr missense_variant 0.15
embB 4246639 c.126G>C synonymous_variant 0.12
aftB 4267950 c.857_886delGGCCGTCGTTCCTGCGTCCCGTGCTGGCAC disruptive_inframe_deletion 0.18
aftB 4268277 p.Pro187Leu missense_variant 0.11
ethR 4327576 p.Ser10Pro missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0