TB-Profiler result

Run: ERR3468561
Summary

Run ID: ERR3468561

Sample name:

Date: 01-04-2023 02:17:42

Number of reads: 36110

Percentage reads mapped: 3.84

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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.83 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.75 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.67 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155693 p.Ser140Asn missense_variant 0.75 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
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
rpoC 764620 c.1251G>C synonymous_variant 1.0
rpoC 764632 c.1263T>C synonymous_variant 1.0
rpoC 764635 c.1266C>T synonymous_variant 1.0
rpoC 764644 c.1275G>C synonymous_variant 1.0
rpoC 764650 c.1281G>T synonymous_variant 1.0
rpoC 764662 c.1293G>C synonymous_variant 1.0
rpoC 764677 c.1308C>G synonymous_variant 0.67
rpoC 764692 c.1323C>T synonymous_variant 0.67
rpoC 764706 p.Leu446Gln missense_variant 0.67
rpoC 764713 c.1344G>C synonymous_variant 0.67
rpoC 764722 c.1353G>C synonymous_variant 0.67
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.6
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.62
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.62
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.25
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.25
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.25
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.33
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.3
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.33
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.25
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.67
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.5
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.67
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.8
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.83
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.83
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.75
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.75
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.75
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.75
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.75
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 1.0
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 1.0
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 1.0
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 1.0
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 1.0
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 1.0
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.75
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.75
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.75
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.75
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.75
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.75
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.67
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 1.0
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 1.0
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 1.0
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 1.0
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 1.0
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 1.0
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.67
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.67
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.5
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.67
rrl 1474717 n.1060_1061insGTCAG non_coding_transcript_exon_variant 0.67
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.67
rrl 1474723 n.1066G>A non_coding_transcript_exon_variant 0.67
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 1.0
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 1.0
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 1.0
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 1.0
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 1.0
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 1.0
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 1.0
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 1.0
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 1.0
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 1.0
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 1.0
rrl 1475762 n.2105G>A non_coding_transcript_exon_variant 1.0
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 1.0
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 1.0
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.75
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.75
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 1.0
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.75
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.75
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.8
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 1.0
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.5
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.6
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.4
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.6
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.44
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.44
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.9
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.42
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.92
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.42
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.36
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.33
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.38
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.55
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.55
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.36
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.36
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.25
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.83
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
katG 2155670 c.442C>T synonymous_variant 1.0
katG 2155674 c.438G>C synonymous_variant 1.0
katG 2155680 c.432G>C synonymous_variant 1.0
katG 2155691 c.421T>C synonymous_variant 0.75
katG 2155696 p.Ala139Gly missense_variant 0.75
katG 2155716 c.396T>G synonymous_variant 0.8
katG 2155728 c.384G>C synonymous_variant 0.8
katG 2155735 p.Met126Gln missense_variant 0.8
katG 2155737 c.375C>A synonymous_variant 0.67
katG 2155743 c.369G>C synonymous_variant 0.67
katG 2155765 p.His116Ala missense_variant 0.6
katG 2155768 p.Ile115Thr missense_variant 0.6
katG 2155785 p.Ala109Ser missense_variant 0.6
katG 2155794 c.318G>C synonymous_variant 0.6
katG 2155800 c.312G>C synonymous_variant 0.6
katG 2155806 c.306T>C synonymous_variant 0.6
katG 2155815 c.297G>C synonymous_variant 0.5
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168043 p.Ala857Val missense_variant 0.67
ald 3087084 c.266delA frameshift_variant 1.0
rpoA 3877623 p.Asp295Glu missense_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
gid 4408237 c.-35C>A upstream_gene_variant 1.0