TB-Profiler result

Run: SRR13861475
Summary

Run ID: SRR13861475

Sample name:

Date: 03-04-2023 09:32:44

Number of reads: 743223

Percentage reads mapped: 14.88

Strain: lineage4.9

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.23 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
gyrA 7877 p.His192Gln missense_variant 1.0
gyrA 8198 c.897T>C synonymous_variant 0.12
mshA 576146 p.Val267Leu missense_variant 1.0
rpoB 759869 c.63C>T synonymous_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.23
rpoB 761129 c.1323G>C synonymous_variant 0.23
rpoB 761133 p.Leu443Ile missense_variant 0.23
rpoB 761150 c.1344A>C synonymous_variant 0.2
rpoB 761151 p.Leu449Val missense_variant 0.2
rpoB 761156 c.1350G>C synonymous_variant 0.19
rpoB 761162 c.1356G>C synonymous_variant 0.2
rpoB 761165 c.1359G>C synonymous_variant 0.19
rpoB 761168 c.1362C>G synonymous_variant 0.19
rpoB 761178 p.Ser458Thr missense_variant 0.17
rpoB 761192 c.1386C>G synonymous_variant 0.17
rpoB 761195 c.1389G>C synonymous_variant 0.17
rpoB 761196 p.Leu464Phe missense_variant 0.17
rpoB 761204 c.1398C>T synonymous_variant 0.19
rpoB 761207 c.1401C>T synonymous_variant 0.19
rpoB 761213 c.1407G>A synonymous_variant 0.19
rpoB 761220 p.Ser472Thr missense_variant 0.19
rpoB 761234 c.1428G>C synonymous_variant 0.19
rpoB 761235 p.Met477Val missense_variant 0.19
rpoC 762920 c.-450C>T upstream_gene_variant 0.12
rpoB 762930 p.Pro1042Ser missense_variant 0.12
rpoB 762942 p.Ile1046Val missense_variant 0.12
rpoC 762995 c.-375G>T upstream_gene_variant 0.12
rpoC 763782 p.Ser138* stop_gained 1.0
rpoC 764568 p.Lys400Thr missense_variant 1.0
mmpL5 777073 p.Lys470Glu missense_variant 1.0
mmpL5 777311 c.1170C>T synonymous_variant 1.0
mmpL5 778981 c.-501C>A upstream_gene_variant 1.0
rplC 801436 p.Ser210Arg missense_variant 1.0
fbiC 1303686 c.756C>G synonymous_variant 1.0
rrs 1472605 n.760G>C non_coding_transcript_exon_variant 0.93
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.28
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.29
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.29
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.28
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.3
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.28
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.28
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.26
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.27
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.27
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.27
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.36
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.31
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.31
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.3
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.31
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.12
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.17
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.54
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.64
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.64
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.64
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.66
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.7
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.7
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.7
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.7
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.7
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.72
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.73
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.73
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.73
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.74
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.73
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.73
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.73
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.73
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.73
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.44
inhA 1674376 p.Pro59Ser missense_variant 1.0
tlyA 1917844 c.-96C>A upstream_gene_variant 1.0
tlyA 1918260 p.His107Gln missense_variant 1.0
katG 2154461 p.Ala551Pro missense_variant 1.0
Rv1979c 2222535 c.630C>G synonymous_variant 1.0
kasA 2518608 p.Met165Thr missense_variant 0.96
eis 2714211 c.1122G>A synonymous_variant 1.0
ahpC 2726250 p.Gly20Arg missense_variant 1.0
fprA 3473932 c.-75G>A upstream_gene_variant 1.0
Rv3236c 3612518 p.Tyr200Ser missense_variant 1.0
fbiB 3641684 p.Ser50Arg missense_variant 1.0
embC 4240263 p.Val134Ala missense_variant 1.0
embC 4240920 p.Leu353Pro missense_variant 1.0
embC 4241504 p.Val548Met missense_variant 1.0
embB 4248000 p.Asp496Val missense_variant 1.0
aftB 4268715 p.Leu41Pro missense_variant 1.0
ethR 4327704 p.Lys52Asn missense_variant 1.0