TB-Profiler result

Run: SRR13861360
Summary

Run ID: SRR13861360

Sample name:

Date: 03-04-2023 09:29:53

Number of reads: 450234

Percentage reads mapped: 45.07

Strain: lineage4.9

Drug-resistance: HR-TB

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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
lineage4.9 Euro-American (H37Rv-like) T1 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
katG 2154798 c.1313_1314insT frameshift_variant 1.0 isoniazid
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
gyrB 5906 p.Val223Leu missense_variant 1.0
gyrB 6011 p.Val258Met missense_variant 1.0
gyrB 6678 p.Pro480Arg missense_variant 1.0
fgd1 490676 c.-107G>C upstream_gene_variant 1.0
ccsA 620028 c.138G>C synonymous_variant 1.0
rpoB 759638 c.-169T>A upstream_gene_variant 1.0
rpoB 760454 c.650delG frameshift_variant 1.0
rpoC 765487 p.Met706Ile missense_variant 1.0
rpsL 781409 c.-151T>A upstream_gene_variant 1.0
fbiC 1302873 c.-58A>T upstream_gene_variant 1.0
rrs 1471874 n.29A>C non_coding_transcript_exon_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.19
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.18
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.18
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.19
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.19
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.19
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.2
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.2
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.21
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.2
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.2
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.19
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.19
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.19
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.18
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.19
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.14
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.14
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.33
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.33
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.32
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.26
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.36
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.38
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.4
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.4
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.38
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.38
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.29
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.29
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.29
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
katG 2154654 p.Ser486Arg missense_variant 1.0
katG 2154882 c.1230G>A synonymous_variant 1.0
katG 2155857 c.255C>A synonymous_variant 1.0
PPE35 2170198 p.Ala139Ser missense_variant 1.0
pncA 2290069 c.-828C>T upstream_gene_variant 1.0
eis 2714922 c.411G>A synonymous_variant 1.0
thyA 3074067 c.405C>G synonymous_variant 1.0
alr 3840223 c.1198A>C synonymous_variant 1.0
alr 3840711 p.Ser237Leu missense_variant 1.0
clpC1 4039648 p.Glu353Gln missense_variant 1.0
embC 4242023 p.Val721Leu missense_variant 1.0
embA 4245071 c.1839G>A synonymous_variant 1.0
ethA 4327364 p.Lys37Arg missense_variant 1.0