TB-Profiler result

Run: SRR13861402

Summary

Run ID: SRR13861402

Sample name:

Date: 03-04-2023 09:30:54

Number of reads: 230091

Percentage reads mapped: 7.68

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
embC 4240748 p.Tyr296His missense_variant 1.0 ethambutol
embB 4247959 p.Met482Ile missense_variant 1.0 ethambutol
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
fgd1 491360 p.Ile193Ser missense_variant 1.0
mshA 576396 p.Ser350Ile missense_variant 1.0
rpoB 760225 p.Glu140Ala missense_variant 1.0
rpoB 761204 c.1398C>T synonymous_variant 0.18
rpoB 761207 c.1401C>T synonymous_variant 0.2
rpoB 761213 c.1407G>A synonymous_variant 0.2
rpoB 761220 p.Ser472Thr missense_variant 0.29
rpoB 761234 c.1428G>C synonymous_variant 0.29
rpoB 761235 p.Met477Val missense_variant 0.25
rpoC 762860 c.-510G>C upstream_gene_variant 0.2
rpoC 762863 c.-507T>C upstream_gene_variant 0.27
rpoB 762878 p.Ile1024Met missense_variant 0.3
rpoB 762879 p.Met1025Leu missense_variant 0.27
rpoB 762888 p.His1028Asn missense_variant 0.3
rpoB 762911 p.Ile1035Met missense_variant 0.3
rpoC 762920 c.-450C>T upstream_gene_variant 0.27
rpoC 762929 c.-441G>C upstream_gene_variant 0.27
rpoB 762930 p.Pro1042Ser missense_variant 0.27
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 0.27
rpoB 762939 p.Met1045Leu missense_variant 0.27
rpoB 762942 p.Ile1046Val missense_variant 0.27
rpoC 762962 c.-408C>T upstream_gene_variant 0.27
rpoC 762971 c.-399G>A upstream_gene_variant 0.27
rpoC 762983 c.-387C>T upstream_gene_variant 0.17
rpoC 762989 c.-381G>C upstream_gene_variant 0.17
rpoC 762995 c.-375G>T upstream_gene_variant 0.18
rpoC 767186 p.Gln1273* stop_gained 1.0
mmpR5 779067 p.Tyr26* stop_gained 1.0
rplC 800933 p.Pro42His missense_variant 1.0
fbiC 1305306 c.2376A>T synonymous_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.25
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.29
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.29
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.25
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.25
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.25
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.25
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.25
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.25
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.25
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.22
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.22
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.22
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.2
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.25
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.25
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.3
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.2
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.42
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.38
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.38
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.38
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.38
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.38
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.42
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.42
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.42
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.42
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.42
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.42
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.45
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.45
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.45
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.45
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.42
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.36
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.36
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.3
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.3
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.46
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.83
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.89
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 0.91
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.9
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.92
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.92
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.92
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.9
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.92
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.92
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.92
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.92
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.92
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.91
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.9
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.89
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.88
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.62
tlyA 1918560 c.621G>T synonymous_variant 1.0
ndh 2102402 p.Leu214Arg missense_variant 1.0
katG 2156175 c.-64T>G upstream_gene_variant 1.0
PPE35 2169349 p.Phe422Ile missense_variant 1.0
PPE35 2170540 p.Leu25Val missense_variant 1.0
pncA 2288999 p.Phe81Leu missense_variant 1.0
fbiD 3339660 c.543C>G synonymous_variant 1.0
Rv3236c 3612627 p.Ala164Thr missense_variant 1.0
embA 4244119 p.Tyr296Phe missense_variant 1.0
embB 4247417 p.Tyr302Asn missense_variant 1.0
embB 4248036 p.Val508Gly missense_variant 1.0
embB 4248325 c.1812G>C synonymous_variant 1.0
aftB 4267894 p.Ile315Phe missense_variant 1.0
ethA 4326052 p.Asp474Glu missense_variant 1.0
ethA 4327388 p.Thr29Ile missense_variant 1.0
ethR 4328162 p.His205Pro missense_variant 1.0
whiB6 4338518 c.4C>A synonymous_variant 1.0