TB-Profiler result

Run: ERR2513628
Summary

Run ID: ERR2513628

Sample name:

Date: 31-03-2023 19:48:16

Number of reads: 818247

Percentage reads mapped: 91.08

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 0.75 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
fgd1 490988 p.Leu69Pro missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 0.94
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575987 c.641delT frameshift_variant 0.13
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762380 c.-990T>A upstream_gene_variant 0.12
rpoC 764389 p.Leu340Phe missense_variant 0.1
rpoC 764405 c.1036A>C synonymous_variant 0.17
rpoC 764431 c.1062G>C synonymous_variant 0.2
rpoC 764434 c.1065A>G synonymous_variant 0.2
rpoC 764446 c.1077T>C synonymous_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766967 p.Pro1200Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776148 p.Ile778Asn missense_variant 0.12
mmpL5 777119 p.His454Gln missense_variant 0.17
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.27
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.36
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.38
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.5
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.4
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.5
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.6
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.71
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.71
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.71
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.71
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.71
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.83
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.7
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.7
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.75
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.83
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.33
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.75
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.75
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.29
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.5
rrs 1472896 n.1051T>C non_coding_transcript_exon_variant 0.25
rrs 1472911 n.1066T>C non_coding_transcript_exon_variant 0.31
rrs 1472918 n.1073A>G non_coding_transcript_exon_variant 0.31
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.15
rrs 1472959 n.1115_1116insGTTAG non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.27
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.3
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.3
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.44
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.4
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.4
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.44
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.18
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.27
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.25
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.22
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.15
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.15
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.38
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.38
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.38
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.33
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.29
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 1.0
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918034 p.Val32Gly missense_variant 0.33
ndh 2103225 c.-183A>C upstream_gene_variant 0.25
katG 2153972 p.Asp714Asn missense_variant 0.1
PPE35 2169902 p.Leu237Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746575 p.Met342Val missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448344 c.-160G>C upstream_gene_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841097 c.324G>C synonymous_variant 0.11
clpC1 4039508 c.1197G>C synonymous_variant 0.1
panD 4043993 p.Arg97Trp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244877 p.Ala549Pro missense_variant 0.14
embA 4245072 p.Leu614Met missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>A upstream_gene_variant 1.0