TB-Profiler result

Run: SRR13861437
Summary

Run ID: SRR13861437

Sample name:

Date: 03-04-2023 09:31:49

Number of reads: 138269

Percentage reads mapped: 2.31

Strain: lineage4.9

Drug-resistance: RR-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
rpoB 761131 p.Gly442Glu missense_variant 0.67 rifampicin
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 6406 p.Asn389Lys missense_variant 1.0
mshA 575880 p.His178Pro missense_variant 1.0
mshA 576356 p.Ala337Ser missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.67
rpoB 761129 c.1323G>C synonymous_variant 0.67
rpoB 761133 p.Leu443Ile missense_variant 0.6
rpoB 761150 c.1344A>C synonymous_variant 0.8
rpoB 761151 p.Leu449Val missense_variant 0.8
rpoB 761156 c.1350G>C synonymous_variant 0.8
rpoB 761162 c.1356G>C synonymous_variant 0.8
rpoB 761165 c.1359G>C synonymous_variant 0.8
rpoB 761168 c.1362C>G synonymous_variant 0.8
rpoB 761178 p.Ser458Thr missense_variant 0.8
rpoB 761192 c.1386C>G synonymous_variant 0.8
rpoB 761195 c.1389G>C synonymous_variant 0.8
rpoB 761196 p.Leu464Phe missense_variant 0.8
rpoB 761204 c.1398C>T synonymous_variant 0.8
rpoB 761207 c.1401C>T synonymous_variant 0.8
rpoB 761213 c.1407G>A synonymous_variant 0.8
rpoB 761220 p.Ser472Thr missense_variant 0.8
rpoB 761234 c.1428G>C synonymous_variant 0.8
rpoB 761235 p.Met477Val missense_variant 0.8
rpoB 762878 p.Ile1024Met missense_variant 0.75
rpoB 762879 p.Met1025Leu missense_variant 0.75
rpoB 762888 p.His1028Asn missense_variant 0.75
rpoB 762911 p.Ile1035Met missense_variant 0.75
rpoC 762920 c.-450C>T upstream_gene_variant 1.0
rpoC 762929 c.-441G>C upstream_gene_variant 1.0
rpoB 762930 p.Pro1042Ser missense_variant 1.0
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 1.0
rpoB 762939 p.Met1045Leu missense_variant 1.0
rpoB 762942 p.Ile1046Val missense_variant 1.0
rpoC 762962 c.-408C>T upstream_gene_variant 1.0
rpoC 762971 c.-399G>A upstream_gene_variant 1.0
rpoC 762983 c.-387C>T upstream_gene_variant 1.0
rpoC 762989 c.-381G>C upstream_gene_variant 0.75
rpoC 762995 c.-375G>T upstream_gene_variant 0.75
fbiC 1303517 p.Met196Arg missense_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.33
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.33
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 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 0.25
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.25
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.25
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.25
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.25
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.25
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.25
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.29
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.56
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.53
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.53
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.53
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.53
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.53
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.53
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.56
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.56
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.56
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.56
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.56
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.64
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.64
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.64
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.64
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.64
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.7
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.64
rrl 1473558 n.-100T>G upstream_gene_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.57
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.96
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.96
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.96
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.95
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.95
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.97
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.97
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.97
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.97
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.97
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.98
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.98
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.99
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.99
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.99
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.99
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.99
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.99
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.99
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.99
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 1.0
fabG1 1673792 p.Arg118Leu missense_variant 1.0
rpsA 1833709 c.168C>T synonymous_variant 1.0
rpsA 1834448 p.Lys303* stop_gained 1.0
tlyA 1918103 p.Val55Ala missense_variant 1.0
tlyA 1918250 p.Gly104Ala missense_variant 1.0
Rv1979c 2222544 c.621G>A synonymous_variant 1.0
eis 2715078 c.255C>G synonymous_variant 1.0
folC 2747750 c.-152G>C upstream_gene_variant 1.0
ald 3086982 p.Ala55Pro missense_variant 1.0
Rv3083 3449935 p.Ile478Val missense_variant 1.0
fbiB 3642147 p.Val205Phe missense_variant 1.0
fbiB 3642189 p.Gly219Trp missense_variant 1.0
clpC1 4039120 p.Ser529Ala missense_variant 1.0
clpC1 4039306 p.Gln467Lys missense_variant 1.0
clpC1 4039400 c.1304delA frameshift_variant 1.0
ethA 4327034 p.Tyr147Phe missense_variant 1.0
gid 4408038 p.Ile55Met missense_variant 1.0