TB-Profiler result

Run: SRR13861588
Summary

Run ID: SRR13861588

Sample name:

Date: 03-04-2023 09:35:39

Number of reads: 916020

Percentage reads mapped: 18.34

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 0.15 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 5417 p.Gly60Ser missense_variant 1.0
gyrB 6381 p.Lys381Arg missense_variant 1.0
fgd1 491364 c.582T>C synonymous_variant 1.0
fgd1 491557 p.Lys259* stop_gained 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.15
rpoB 761129 c.1323G>C synonymous_variant 0.15
rpoB 761133 p.Leu443Ile missense_variant 0.15
rpoB 761150 c.1344A>C synonymous_variant 0.14
rpoB 761151 p.Leu449Val missense_variant 0.14
rpoB 761156 c.1350G>C synonymous_variant 0.14
rpoB 761162 c.1356G>C synonymous_variant 0.14
rpoB 761165 c.1359G>C synonymous_variant 0.14
rpoB 761168 c.1362C>G synonymous_variant 0.14
rpoB 761178 p.Ser458Thr missense_variant 0.15
rpoB 761192 c.1386C>G synonymous_variant 0.18
rpoB 761195 c.1389G>C synonymous_variant 0.15
rpoB 761196 p.Leu464Phe missense_variant 0.15
rpoB 761204 c.1398C>T synonymous_variant 0.13
rpoB 761207 c.1401C>T synonymous_variant 0.13
rpoB 761213 c.1407G>A synonymous_variant 0.13
rpoB 761220 p.Ser472Thr missense_variant 0.14
rpoB 761234 c.1428G>C synonymous_variant 0.15
rpoB 761235 p.Met477Val missense_variant 0.14
Rv1258c 1406579 c.762C>T synonymous_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.33
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.28
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.3
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.33
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.31
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.31
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.32
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.33
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.31
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.32
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.27
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.3
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.32
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.32
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.33
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.19
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.19
rrl 1473445 n.-213G>T upstream_gene_variant 1.0
rrl 1475387 n.1730C>T non_coding_transcript_exon_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.54
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.61
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.62
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.6
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.63
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.66
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.66
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.65
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.65
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.65
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.64
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.64
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.65
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.63
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.65
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.64
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.63
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.63
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.61
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.59
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
fabG1 1673735 p.Arg99Leu missense_variant 1.0
inhA 1674246 c.45C>T synonymous_variant 1.0
inhA 1674937 c.736C>T synonymous_variant 1.0
rpsA 1833345 c.-196delC upstream_gene_variant 1.0
PPE35 2170775 c.-163T>A upstream_gene_variant 1.0
pncA 2289663 c.-422A>G upstream_gene_variant 1.0
pncA 2290143 c.-903_-902insG upstream_gene_variant 1.0
eis 2714984 p.Ala117Thr missense_variant 1.0
ahpC 2726534 c.342C>T synonymous_variant 1.0
thyA 3074240 p.Thr78Ser missense_variant 1.0
ald 3086806 c.-14_-13insA upstream_gene_variant 1.0
Rv3083 3448862 p.Gly120Ala missense_variant 1.0
fprA 3473896 c.-110delA upstream_gene_variant 1.0
alr 3840667 p.Arg252Gly missense_variant 1.0
rpoA 3878142 c.366C>G synonymous_variant 1.0
clpC1 4040117 p.Glu196Asp missense_variant 1.0
embA 4242988 c.-245A>G upstream_gene_variant 1.0
ubiA 4269624 p.Tyr70* stop_gained 1.0
ethR 4328039 p.Arg164Pro missense_variant 1.0
whiB6 4338235 p.Arg96Leu missense_variant 1.0