TB-Profiler result

Run: SRR13861178
Summary

Run ID: SRR13861178

Sample name:

Date: 03-04-2023 09:25:23

Number of reads: 212757

Percentage reads mapped: 7.1

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 0.38 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
rpoB 759613 c.-194C>A upstream_gene_variant 1.0
rpoB 759854 p.Ser16Arg missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.38
rpoB 761129 c.1323G>C synonymous_variant 0.38
rpoB 761133 p.Leu443Ile missense_variant 0.38
rpoB 761150 c.1344A>C synonymous_variant 0.33
rpoB 761151 p.Leu449Val missense_variant 0.38
rpoB 761156 c.1350G>C synonymous_variant 0.33
rpoB 761162 c.1356G>C synonymous_variant 0.38
rpoB 761165 c.1359G>C synonymous_variant 0.38
rpoB 761168 c.1362C>G synonymous_variant 0.38
rpoB 761178 p.Ser458Thr missense_variant 0.43
rpoB 761192 c.1386C>G synonymous_variant 0.5
rpoB 761195 c.1389G>C synonymous_variant 0.5
rpoB 761196 p.Leu464Phe missense_variant 0.5
rpoB 761204 c.1398C>T synonymous_variant 0.5
rpoB 761207 c.1401C>T synonymous_variant 0.6
rpoB 761213 c.1407G>A synonymous_variant 0.6
rpoB 761220 p.Ser472Thr missense_variant 0.6
rpoB 761234 c.1428G>C synonymous_variant 0.5
rpoB 761235 p.Met477Val missense_variant 0.5
rpoB 762878 p.Ile1024Met missense_variant 0.5
rpoB 762879 p.Met1025Leu missense_variant 0.5
rpoB 762888 p.His1028Asn missense_variant 0.4
rpoB 762911 p.Ile1035Met missense_variant 0.4
rpoC 762920 c.-450C>T upstream_gene_variant 0.4
rpoC 762929 c.-441G>C upstream_gene_variant 0.33
rpoB 762930 p.Pro1042Ser missense_variant 0.33
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 0.29
rpoB 762939 p.Met1045Leu missense_variant 0.29
rpoB 762942 p.Ile1046Val missense_variant 0.33
rpoC 762962 c.-408C>T upstream_gene_variant 0.33
rpoC 762971 c.-399G>A upstream_gene_variant 0.33
rpoC 762983 c.-387C>T upstream_gene_variant 0.33
rpoC 762989 c.-381G>C upstream_gene_variant 0.33
rpoC 762995 c.-375G>T upstream_gene_variant 0.33
rpoC 765119 p.Gly584Arg missense_variant 1.0
rpoC 766845 p.Arg1159His missense_variant 1.0
mmpL5 776280 p.Arg734His missense_variant 1.0
mmpR5 778208 c.-782C>G upstream_gene_variant 1.0
fbiC 1305195 c.2265T>G synonymous_variant 1.0
Rv1258c 1406120 c.1221C>T synonymous_variant 1.0
embR 1417526 c.-180delA upstream_gene_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.5
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.5
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.5
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.5
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.47
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.47
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.5
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.5
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.5
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.5
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.5
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.5
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.5
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.43
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.33
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.33
rrl 1473960 n.303T>G non_coding_transcript_exon_variant 1.0
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.29
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.44
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 0.89
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.89
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.88
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.87
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.87
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.87
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.87
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.87
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.88
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.88
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.88
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.88
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.9
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.9
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.88
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.88
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.85
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.84
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.52
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.33
rpsA 1833623 c.82_83insG frameshift_variant 1.0
tlyA 1918515 c.576C>T synonymous_variant 1.0
tlyA 1918620 c.681C>A synonymous_variant 1.0
katG 2155055 p.Tyr353Asn missense_variant 1.0
PPE35 2169626 c.987C>T synonymous_variant 1.0
eis 2714776 p.Val186Glu missense_variant 1.0
ahpC 2726084 c.-109C>A upstream_gene_variant 1.0
Rv2752c 3065052 p.Glu380Asp missense_variant 1.0
Rv2752c 3065097 c.1095C>T synonymous_variant 1.0
thyA 3073902 c.570C>G synonymous_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.29
panD 4044175 p.Ala36Asp missense_variant 1.0
embC 4240583 p.Thr241Ala missense_variant 1.0
whiB6 4338609 c.-88T>G upstream_gene_variant 1.0
gid 4407696 c.507C>T synonymous_variant 1.0