TB-Profiler result

Run: SRR13861713
Summary

Run ID: SRR13861713

Sample name:

Date: 03-04-2023 09:38:41

Number of reads: 281823

Percentage reads mapped: 14.1

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 0.3 rifampicin
pncA 2288784 p.Thr153Asn missense_variant 1.0 pyrazinamide
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 8486 c.1185T>C synonymous_variant 0.14
gyrA 9494 p.Tyr731* stop_gained 1.0
fgd1 491771 p.Pro330Leu missense_variant 1.0
rpoB 760235 c.429T>C synonymous_variant 0.18
rpoB 760283 c.477G>C synonymous_variant 0.14
rpoB 760307 c.501T>C synonymous_variant 0.18
rpoB 760328 c.522G>C synonymous_variant 0.18
rpoB 760331 c.525G>C synonymous_variant 0.18
rpoB 760337 c.531C>G synonymous_variant 0.18
rpoB 760340 c.534G>C synonymous_variant 0.18
rpoB 760361 c.555T>C synonymous_variant 0.18
rpoB 761126 c.1320G>T synonymous_variant 0.27
rpoB 761129 c.1323G>C synonymous_variant 0.3
rpoB 761133 p.Leu443Ile missense_variant 0.3
rpoB 761150 c.1344A>C synonymous_variant 0.3
rpoB 761151 p.Leu449Val missense_variant 0.3
rpoB 761156 c.1350G>C synonymous_variant 0.3
rpoB 761162 c.1356G>C synonymous_variant 0.25
rpoB 761165 c.1359G>C synonymous_variant 0.33
rpoB 761168 c.1362C>G synonymous_variant 0.33
rpoB 761178 p.Ser458Thr missense_variant 0.25
rpoB 761192 c.1386C>G synonymous_variant 0.23
rpoB 761195 c.1389G>C synonymous_variant 0.21
rpoB 761196 p.Leu464Phe missense_variant 0.23
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 0.23
rpoB 761220 p.Ser472Thr missense_variant 0.23
rpoB 761234 c.1428G>C synonymous_variant 0.23
rpoB 761235 p.Met477Val missense_variant 0.23
rpoC 762860 c.-510G>C upstream_gene_variant 0.5
rpoC 762863 c.-507T>C upstream_gene_variant 0.5
rpoB 762878 p.Ile1024Met missense_variant 0.57
rpoB 762879 p.Met1025Leu missense_variant 0.57
rpoB 762888 p.His1028Asn missense_variant 0.5
rpoB 762911 p.Ile1035Met missense_variant 0.4
rpoC 762920 c.-450C>T upstream_gene_variant 0.36
rpoC 762929 c.-441G>C upstream_gene_variant 0.45
rpoB 762930 p.Pro1042Ser missense_variant 0.36
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 0.36
rpoB 762939 p.Met1045Leu missense_variant 0.36
rpoB 762942 p.Ile1046Val missense_variant 0.36
rpoB 762948 p.Gln1048Glu missense_variant 0.55
rpoC 762962 c.-408C>T upstream_gene_variant 0.33
rpoC 762971 c.-399G>A upstream_gene_variant 0.33
rpoC 762983 c.-387C>T upstream_gene_variant 0.33
rpoC 762989 c.-381G>C upstream_gene_variant 0.55
rpoC 762995 c.-375G>T upstream_gene_variant 0.55
rpoC 763028 c.-342T>C upstream_gene_variant 0.29
rpoC 763031 c.-339T>G upstream_gene_variant 0.25
rpoC 763034 c.-336C>G upstream_gene_variant 0.25
rpoC 763040 c.-330C>G upstream_gene_variant 0.29
rpoC 767026 c.3657G>C synonymous_variant 1.0
fbiC 1303155 c.225G>C synonymous_variant 1.0
fbiC 1304225 p.Gly432Asp missense_variant 1.0
fbiC 1305046 p.Ser706Pro missense_variant 1.0
Rv1258c 1406433 c.907delA frameshift_variant 1.0
embR 1416546 p.Thr268Ser missense_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.46
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.43
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.43
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.46
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.5
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.5
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.5
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.5
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.5
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.5
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.47
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.47
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.5
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.5
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.47
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.36
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.36
rrl 1474652 n.995T>G non_coding_transcript_exon_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.22
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.59
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.68
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.68
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.68
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.68
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.73
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 0.73
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 0.72
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.72
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.72
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.71
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.71
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.69
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.68
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
ndh 2102315 p.Ile243Thr missense_variant 1.0
kasA 2518563 p.Ala150Gly missense_variant 1.0
kasA 2519015 p.Ser301Ala missense_variant 1.0
fprA 3473934 c.-73G>C upstream_gene_variant 0.29
Rv3236c 3612913 p.Leu68Phe missense_variant 1.0
embC 4239676 c.-187T>C upstream_gene_variant 0.29
ethA 4326245 p.Asp410Ala missense_variant 1.0
ethR 4327132 c.-417G>A upstream_gene_variant 1.0
ethA 4327893 c.-420C>A upstream_gene_variant 1.0
gid 4408070 p.Trp45Arg missense_variant 1.0