TB-Profiler result

Run: ERR4815655
Summary

Run ID: ERR4815655

Sample name:

Date: 01-04-2023 13:59:18

Number of reads: 846583

Percentage reads mapped: 95.98

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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 0.5 streptomycin
pncA 2289166 c.75delC frameshift_variant 0.14 pyrazinamide
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 7323 p.Pro8Ala missense_variant 1.0
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 491591 p.Lys270Met missense_variant 1.0
rpoB 759690 c.-117G>A upstream_gene_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761302 p.Arg499Pro missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776033 p.Phe816Leu missense_variant 0.13
mmpL5 776659 p.Asp608Asn missense_variant 1.0
mmpR5 779266 p.Phe93Leu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471656 n.-190G>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.25
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.5
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.6
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.6
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.62
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.62
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.62
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.43
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.67
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.5
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.5
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.38
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.67
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.4
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.6
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.6
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.5
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.5
rrl 1476194 n.2537A>T non_coding_transcript_exon_variant 0.5
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.67
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.67
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.67
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rpsA 1834606 c.1065C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103001 c.42G>A synonymous_variant 0.13
katG 2155931 p.Ala61Ser missense_variant 0.12
PPE35 2168501 p.Phe704Leu missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714385 p.Glu316Asp missense_variant 0.12
thyA 3074255 p.His73Tyr missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087469 c.651delT frameshift_variant 0.1
Rv3083 3449720 p.Leu406Pro missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247121 p.Ser203Leu missense_variant 1.0
embB 4249694 c.3185dupG frameshift_variant 0.11
aftB 4268807 c.30G>T synonymous_variant 1.0
ethR 4327626 p.Glu26Asp missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0