TB-Profiler result

Run: SRR13861337
Summary

Run ID: SRR13861337

Sample name:

Date: 03-04-2023 09:29:24

Number of reads: 587919

Percentage reads mapped: 14.71

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 0.18 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
fgd1 490955 p.Met58Arg missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.18
rpoB 761129 c.1323G>C synonymous_variant 0.18
rpoB 761133 p.Leu443Ile missense_variant 0.18
rpoB 761150 c.1344A>C synonymous_variant 0.2
rpoB 761151 p.Leu449Val missense_variant 0.19
rpoB 761156 c.1350G>C synonymous_variant 0.2
rpoB 761162 c.1356G>C synonymous_variant 0.2
rpoB 761165 c.1359G>C synonymous_variant 0.2
rpoB 761168 c.1362C>G synonymous_variant 0.21
rpoB 761178 p.Ser458Thr missense_variant 0.24
rpoB 761192 c.1386C>G synonymous_variant 0.24
rpoB 761195 c.1389G>C synonymous_variant 0.24
rpoB 761196 p.Leu464Phe missense_variant 0.24
rpoB 761204 c.1398C>T synonymous_variant 0.25
rpoB 761207 c.1401C>T synonymous_variant 0.25
rpoB 761213 c.1407G>A synonymous_variant 0.25
rpoB 761220 p.Ser472Thr missense_variant 0.25
rpoB 761234 c.1428G>C synonymous_variant 0.24
rpoB 761235 p.Met477Val missense_variant 0.24
rpoC 764387 c.1018T>C synonymous_variant 0.15
rpoC 764401 c.1032C>T synonymous_variant 0.22
rpoC 764404 c.1035C>T synonymous_variant 0.22
rpoC 764405 c.1036A>C synonymous_variant 0.22
rpoC 764419 c.1050C>T synonymous_variant 0.23
rpoC 764428 c.1059G>T synonymous_variant 0.25
rpoC 764434 c.1065A>G synonymous_variant 0.24
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.23
rpoC 764441 p.Ile358Leu missense_variant 0.22
rpoC 764446 c.1077T>C synonymous_variant 0.23
rpoC 764451 p.Gly361Ala missense_variant 0.23
rpoC 764455 c.1086G>T synonymous_variant 0.24
rpoC 764461 p.Glu364Asp missense_variant 0.24
rpoC 764470 c.1101C>G synonymous_variant 0.24
rpoC 764471 p.Asn368Arg missense_variant 0.19
rpoC 764479 c.1110G>A synonymous_variant 0.24
rpoC 764485 c.1116G>C synonymous_variant 0.25
rpoC 764498 p.Ser377Ala missense_variant 0.25
rpoC 764503 c.1134G>C synonymous_variant 0.24
rpoC 764509 c.1140G>C synonymous_variant 0.24
rpoC 764513 p.Phe382Leu missense_variant 0.23
rpoC 764521 c.1152T>C synonymous_variant 0.15
mmpS5 779639 c.-735dupG upstream_gene_variant 1.0
fbiC 1304529 c.1599T>C synonymous_variant 1.0
Rv1258c 1406845 p.Ala166Pro missense_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.37
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.32
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.32
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.32
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.3
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.25
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.29
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.28
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.28
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.3
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.3
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.35
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.35
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.37
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.37
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.32
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.16
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.16
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.24
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.74
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.79
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.79
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.79
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.79
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.79
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.81
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.8
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.8
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.8
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.8
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.8
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.83
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.82
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.77
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.78
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.76
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.76
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.43
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.22
inhA 1674607 p.Pro136Ser missense_variant 1.0
inhA 1674778 p.Pro193Ala missense_variant 1.0
PPE35 2169081 p.Leu511Ser missense_variant 1.0
PPE35 2169202 p.Ser471Pro missense_variant 1.0
Rv1979c 2222091 c.1074G>T synonymous_variant 1.0
Rv1979c 2223306 c.-142T>A upstream_gene_variant 1.0
pncA 2289228 p.Ile5Asn missense_variant 1.0
kasA 2518176 p.Ala21Gly missense_variant 1.0
eis 2714755 p.Pro193Gln missense_variant 1.0
ahpC 2726324 c.132A>G synonymous_variant 1.0
ahpC 2726362 p.Phe57Ser missense_variant 1.0
pepQ 2859580 p.Leu280Arg missense_variant 1.0
pepQ 2859999 c.420G>T synonymous_variant 1.0
thyX 3067940 c.6C>G synonymous_variant 1.0
thyA 3074620 c.-149C>A upstream_gene_variant 1.0
fprA 3473861 c.-146T>G upstream_gene_variant 1.0
fprA 3474953 p.Gln316Arg missense_variant 1.0
ddn 3986889 p.Phe16Val missense_variant 1.0
embC 4242041 p.Met727Leu missense_variant 1.0
embA 4244723 p.Gln497His missense_variant 1.0
aftB 4267979 c.858G>C synonymous_variant 1.0