TB-Profiler result

Run: ERR4818890
Summary

Run ID: ERR4818890

Sample name:

Date: 01-04-2023 15:48:32

Number of reads: 300112

Percentage reads mapped: 95.83

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 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 0.44 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.27 streptomycin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.2 kanamycin, capreomycin, aminoglycosides, amikacin
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 8609 c.1308G>A synonymous_variant 0.2
rpoB 759931 p.Leu42His missense_variant 0.13
rpoB 760926 p.Thr374Pro missense_variant 0.29
rpoC 762575 c.-795C>T upstream_gene_variant 0.22
rpoB 763169 p.Glu1121Asp missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777423 p.Leu353Arg missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.33
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.33
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.33
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.33
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.6
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.67
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.75
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.4
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.4
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.4
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.33
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.43
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.57
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.5
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.5
rrs 1472674 n.829T>A non_coding_transcript_exon_variant 0.33
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.5
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.43
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.38
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.18
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.55
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.25
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.23
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.23
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.62
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.29
rrs 1472916 n.1071A>G non_coding_transcript_exon_variant 0.33
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.5
rrs 1472955 n.1110C>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 1472973 n.1128A>T non_coding_transcript_exon_variant 0.46
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.44
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.44
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.44
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.5
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.48
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.41
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.37
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.3
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.33
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.35
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.37
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.33
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.33
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.35
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.35
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.33
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.29
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.33
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.22
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.25
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.25
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.67
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.33
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.4
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.4
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.5
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.64
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.6
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.44
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.44
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918502 p.Gly188Val missense_variant 0.25
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2169820 p.Asn265Asp missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.25
folC 2746259 p.Val447Gly missense_variant 0.33
folC 2746265 p.Ser445Leu missense_variant 0.4
thyX 3067720 p.Ala76Thr missense_variant 0.25
whiB7 3568539 c.140delC frameshift_variant 0.33
clpC1 4040457 c.247delC frameshift_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245634 p.Lys801Thr missense_variant 0.33
embB 4249732 c.3219C>G synonymous_variant 1.0
aftB 4268453 c.384G>A synonymous_variant 0.25
ethR 4327768 p.Thr74Pro missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0