TB-Profiler result

Run: SRR13861149
Summary

Run ID: SRR13861149

Sample name:

Date: 03-04-2023 09:24:42

Number of reads: 201978

Percentage reads mapped: 3.37

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 0.75 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 5532 c.295dupG frameshift_variant 1.0
gyrB 5832 p.Ala198Gly missense_variant 1.0
gyrA 6976 c.-326A>G upstream_gene_variant 1.0
ccsA 619735 c.-156G>C upstream_gene_variant 1.0
ccsA 620100 c.210G>T synonymous_variant 1.0
rpoB 759609 c.-198C>A upstream_gene_variant 1.0
rpoB 761102 c.1296A>G synonymous_variant 0.5
rpoB 761126 c.1320G>T synonymous_variant 0.75
rpoB 761129 c.1323G>C synonymous_variant 0.75
rpoB 761133 p.Leu443Ile missense_variant 0.75
rpoB 761150 c.1344A>C synonymous_variant 0.82
rpoB 761151 p.Leu449Val missense_variant 0.82
rpoB 761156 c.1350G>C synonymous_variant 0.82
rpoB 761162 c.1356G>C synonymous_variant 0.82
rpoB 761165 c.1359G>C synonymous_variant 0.82
rpoB 761168 c.1362C>G synonymous_variant 0.82
rpoB 761178 p.Ser458Thr missense_variant 0.82
rpoB 761192 c.1386C>G synonymous_variant 0.82
rpoB 761195 c.1389G>C synonymous_variant 0.82
rpoB 761196 p.Leu464Phe missense_variant 0.82
rpoB 761204 c.1398C>T synonymous_variant 0.75
rpoB 761207 c.1401C>T synonymous_variant 0.75
rpoB 761213 c.1407G>A synonymous_variant 0.75
rpoB 761220 p.Ser472Thr missense_variant 0.75
rpoB 761234 c.1428G>C synonymous_variant 0.75
rpoB 761235 p.Met477Val missense_variant 0.75
rpoC 762860 c.-510G>C upstream_gene_variant 0.4
rpoC 762863 c.-507T>C upstream_gene_variant 0.4
rpoB 762878 p.Ile1024Met missense_variant 0.5
rpoB 762879 p.Met1025Leu missense_variant 0.5
rpoB 762888 p.His1028Asn missense_variant 0.5
rpoB 762911 p.Ile1035Met missense_variant 0.5
rpoC 762920 c.-450C>T upstream_gene_variant 0.6
rpoC 762929 c.-441G>C upstream_gene_variant 0.5
rpoB 762930 p.Pro1042Ser missense_variant 0.5
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 0.5
rpoB 762939 p.Met1045Leu missense_variant 0.43
rpoB 762942 p.Ile1046Val missense_variant 0.43
rpoC 762962 c.-408C>T upstream_gene_variant 0.6
rpoC 762971 c.-399G>A upstream_gene_variant 0.5
rpoC 762983 c.-387C>T upstream_gene_variant 0.5
rpoC 762989 c.-381G>C upstream_gene_variant 0.5
rpoC 762995 c.-375G>T upstream_gene_variant 0.5
rpoC 763050 c.-320C>T upstream_gene_variant 1.0
rpoC 764387 c.1018T>C synonymous_variant 0.4
rpoC 764401 c.1032C>T synonymous_variant 0.5
rpoC 764404 c.1035C>T synonymous_variant 0.5
rpoC 764405 c.1036A>C synonymous_variant 0.5
rpoC 764419 c.1050C>T synonymous_variant 0.44
rpoC 764428 c.1059G>T synonymous_variant 0.44
rpoC 764434 c.1065A>G synonymous_variant 0.57
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.57
rpoC 764441 p.Ile358Leu missense_variant 0.57
rpoC 764446 c.1077T>C synonymous_variant 0.5
rpoC 764451 p.Gly361Ala missense_variant 0.5
rpoC 764455 c.1086G>T synonymous_variant 0.5
rpoC 764461 p.Glu364Asp missense_variant 0.5
rpoC 764470 c.1101C>G synonymous_variant 0.5
rpoC 764471 p.Asn368Arg missense_variant 0.5
rpoC 764479 c.1110G>A synonymous_variant 0.5
rpoC 764485 c.1116G>C synonymous_variant 0.5
rpoC 764498 p.Ser377Ala missense_variant 0.5
rpoC 764503 c.1134G>C synonymous_variant 0.5
rpoC 764509 c.1140G>C synonymous_variant 0.5
rpoC 764513 p.Phe382Leu missense_variant 0.5
rpoC 764521 c.1152T>C synonymous_variant 0.5
rpoC 764527 c.1158C>T synonymous_variant 0.33
mmpL5 776796 p.Val562Ala missense_variant 1.0
mmpS5 779584 c.-679A>C upstream_gene_variant 0.29
Rv1258c 1407009 p.Ala111Asp missense_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.18
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.2
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.2
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.22
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.22
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.22
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.22
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.33
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.22
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.22
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.22
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.22
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.22
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.22
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.2
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.18
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.25
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.29
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.22
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.4
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.29
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.29
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.75
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.77
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.77
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.8
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.8
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.81
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.74
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.78
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.74
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.78
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.78
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.78
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.81
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.81
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.81
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.81
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.84
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.76
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.76
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.33
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.33
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.4
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.4
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.45
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.92
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.91
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.9
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.89
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.9
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.94
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.95
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.95
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.95
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.93
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.93
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.92
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.92
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.92
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.92
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.93
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.92
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.93
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.93
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.78
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.54
inhA 1674891 p.Trp230Cys missense_variant 1.0
tlyA 1918625 p.Pro229Leu missense_variant 1.0
Rv1979c 2222721 c.444G>C synonymous_variant 1.0
ahpC 2726345 p.Phe51Leu missense_variant 1.0
Rv2752c 3067095 c.-904G>C upstream_gene_variant 1.0
Rv3083 3448912 p.Ile137Phe missense_variant 1.0
fprA 3474133 p.Pro43Thr missense_variant 1.0
whiB7 3568676 p.Ser2Ala missense_variant 1.0
alr 3840783 c.637_638insT frameshift_variant 1.0
clpC1 4038326 p.Glu793Asp missense_variant 1.0
embC 4241026 c.1164C>G synonymous_variant 1.0
embA 4242250 c.-983C>G upstream_gene_variant 1.0
embB 4247398 c.885G>T synonymous_variant 1.0
aftB 4267490 c.1347G>C synonymous_variant 1.0
ethA 4326203 p.Ser424* stop_gained 1.0