TB-Profiler result

Run: SRR13861364
Summary

Run ID: SRR13861364

Sample name:

Date: 03-04-2023 09:29:58

Number of reads: 90084

Percentage reads mapped: 4.51

Strain: lineage4.9

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
lineage4.9 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
ethA 4326568 c.905delT frameshift_variant 1.0 ethionamide
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 8820 p.Asp507His missense_variant 0.67
rpoB 759961 p.Thr52Asn missense_variant 1.0
rpoB 763050 p.Leu1082Met missense_variant 1.0
mmpL5 775701 p.Pro927Gln missense_variant 1.0
mmpL5 778828 c.-348G>A upstream_gene_variant 1.0
rplC 801353 p.Val182Ala missense_variant 1.0
fbiC 1304512 p.Val528Ile missense_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.55
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.55
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.55
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.55
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.55
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.55
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.6
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.67
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.6
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.6
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.55
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.55
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.6
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.55
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.55
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.55
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.55
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.5
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.5
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.33
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.85
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.91
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.91
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.91
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.95
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.95
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.95
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.95
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.95
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.95
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.95
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.95
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.95
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.93
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.95
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.95
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.97
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.97
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.89
rpsA 1834175 p.Arg212* stop_gained 1.0
Rv1979c 2222085 c.1080G>C synonymous_variant 1.0
folC 2746135 c.1464A>C stop_lost&splice_region_variant 1.0
clpC1 4040066 c.639G>T synonymous_variant 1.0
embC 4241259 c.1397_1398insT frameshift_variant 1.0
embA 4243358 c.126C>T synonymous_variant 1.0
embA 4243469 c.237C>T synonymous_variant 1.0
embB 4248436 c.1923C>T synonymous_variant 1.0
ubiA 4269557 p.Ala93Pro missense_variant 1.0