TB-Profiler result

Run: SRR13861618
Summary

Run ID: SRR13861618

Sample name:

Date: 03-04-2023 09:36:23

Number of reads: 163905

Percentage reads mapped: 3.28

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 0.78 rifampicin
ethA 4327340 p.Trp45* stop_gained 1.0 ethionamide
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 8646 p.Gln449Lys missense_variant 1.0
gyrA 9138 p.Gln613Lys missense_variant 1.0
gyrA 9604 p.Val768Ala missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.78
rpoB 761129 c.1323G>C synonymous_variant 0.78
rpoB 761133 p.Leu443Ile missense_variant 0.78
rpoB 761150 c.1344A>C synonymous_variant 0.78
rpoB 761151 p.Leu449Val missense_variant 0.78
rpoB 761156 c.1350G>C synonymous_variant 0.78
rpoB 761162 c.1356G>C synonymous_variant 0.78
rpoB 761165 c.1359G>C synonymous_variant 0.7
rpoB 761168 c.1362C>G synonymous_variant 0.7
rpoB 761178 p.Ser458Thr missense_variant 0.7
rpoB 761192 c.1386C>G synonymous_variant 0.56
rpoB 761195 c.1389G>C synonymous_variant 0.64
rpoB 761196 p.Leu464Phe missense_variant 0.64
rpoB 761204 c.1398C>T synonymous_variant 0.64
rpoB 761207 c.1401C>T synonymous_variant 0.64
rpoB 761213 c.1407G>A synonymous_variant 0.64
rpoB 761220 p.Ser472Thr missense_variant 0.64
rpoB 761234 c.1428G>C synonymous_variant 0.64
rpoB 761235 p.Met477Val missense_variant 0.64
rpoB 761853 p.Ile683Val missense_variant 1.0
rpoB 762878 p.Ile1024Met missense_variant 0.43
rpoB 762879 p.Met1025Leu missense_variant 0.43
rpoB 762888 p.His1028Asn missense_variant 0.43
rpoB 762911 p.Ile1035Met missense_variant 0.43
rpoC 762920 c.-450C>T upstream_gene_variant 0.43
rpoC 762929 c.-441G>C upstream_gene_variant 0.43
rpoB 762930 p.Pro1042Ser missense_variant 0.43
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 0.5
rpoB 762939 p.Met1045Leu missense_variant 0.5
rpoB 762942 p.Ile1046Val missense_variant 0.5
rpoC 762962 c.-408C>T upstream_gene_variant 0.6
rpoC 762971 c.-399G>A upstream_gene_variant 0.6
rpoC 762983 c.-387C>T upstream_gene_variant 0.6
rpoC 762989 c.-381G>C upstream_gene_variant 0.6
rpoC 762995 c.-375G>T upstream_gene_variant 0.6
rpoC 764387 c.1018T>C synonymous_variant 0.44
rpoC 764401 c.1032C>T synonymous_variant 0.62
rpoC 764404 c.1035C>T synonymous_variant 0.62
rpoC 764405 c.1036A>C synonymous_variant 0.62
rpoC 764419 c.1050C>T synonymous_variant 0.62
rpoC 764428 c.1059G>T synonymous_variant 0.62
rpoC 764434 c.1065A>G synonymous_variant 0.67
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.67
rpoC 764441 p.Ile358Leu missense_variant 0.73
rpoC 764446 c.1077T>C synonymous_variant 0.73
rpoC 764451 p.Gly361Ala missense_variant 0.67
rpoC 764455 c.1086G>T synonymous_variant 0.73
rpoC 764461 p.Glu364Asp missense_variant 0.67
rpoC 764470 c.1101C>G synonymous_variant 0.73
rpoC 764471 p.Asn368Arg missense_variant 0.73
rpoC 764479 c.1110G>A synonymous_variant 0.8
rpoC 764485 c.1116G>C synonymous_variant 0.8
rpoC 764498 p.Ser377Ala missense_variant 0.8
rpoC 764503 c.1134G>C synonymous_variant 0.8
rpoC 764509 c.1140G>C synonymous_variant 0.8
rpoC 764513 p.Phe382Leu missense_variant 0.89
rpoC 764521 c.1152T>C synonymous_variant 0.8
rpoC 764527 c.1158C>T synonymous_variant 0.67
mmpL5 777509 c.972G>T synonymous_variant 1.0
mmpS5 779508 c.-603G>C upstream_gene_variant 1.0
Rv1258c 1406904 c.436dupT frameshift_variant 1.0
Rv1258c 1407127 p.Arg72Ser missense_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.5
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.5
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.5
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.5
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.5
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.5
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.5
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.5
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.5
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.5
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.5
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.5
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.57
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.67
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.67
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.67
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.67
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.57
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.63
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.67
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.67
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.71
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.61
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.63
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.63
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 1.0
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.6
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.63
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.58
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.63
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.63
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.63
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.63
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.63
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.63
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.71
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.67
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.67
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.38
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.38
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.55
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.94
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.93
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.92
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.92
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.93
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 0.96
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.96
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.96
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.96
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.95
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.96
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.96
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.97
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.95
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.95
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.95
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.79
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.5
inhA 1674552 c.351C>G synonymous_variant 1.0
rpsA 1834079 p.Arg180Cys missense_variant 1.0
Rv1979c 2221876 p.Val430Glu missense_variant 1.0
kasA 2518036 c.-78delG upstream_gene_variant 1.0
kasA 2518088 c.-27T>A upstream_gene_variant 1.0
eis 2714449 p.Trp295Ser missense_variant 1.0
eis 2714773 p.Pro187Gln missense_variant 1.0
eis 2715525 c.-193G>T upstream_gene_variant 1.0
ahpC 2726611 c.419_420insA frameshift_variant 1.0
pepQ 2859723 c.696T>C synonymous_variant 1.0
ribD 2987540 c.702G>T synonymous_variant 1.0
fbiD 3339321 c.204G>A synonymous_variant 1.0
fprA 3474339 p.Met111Ile missense_variant 1.0
fprA 3474353 c.348delT frameshift_variant 1.0
clpC1 4038436 p.Ala757Ser missense_variant 1.0
embC 4242635 p.Ala925Ser missense_variant 1.0
embB 4249145 c.2634delC frameshift_variant 1.0
ubiA 4269803 p.Ala11Pro missense_variant 1.0
ethA 4326689 p.Lys262Thr missense_variant 1.0
ethA 4326849 p.Pro209Thr missense_variant 1.0