TB-Profiler result

Run: SRR18572454
Summary

Run ID: SRR18572454

Sample name:

Date: 03-04-2023 19:55:31

Number of reads: 4730903

Percentage reads mapped: 89.63

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 761127 p.Ser441Ala missense_variant 0.11 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.17 kanamycin, capreomycin, aminoglycosides, amikacin
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
rpoB 761051 c.1245G>C synonymous_variant 0.11
rpoB 761054 c.1248G>C synonymous_variant 0.11
rpoB 761060 c.1254C>G synonymous_variant 0.11
rpoB 761084 c.1278C>G synonymous_variant 0.12
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.12
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.12
rpoB 761102 c.1296A>G synonymous_variant 0.13
rpoB 761132 c.1326G>C synonymous_variant 0.1
rpoB 761133 c.1327T>C synonymous_variant 0.1
rpoB 762114 p.Ile770Val missense_variant 0.11
rpoB 762122 p.Asp772Glu missense_variant 0.1
rpoB 762125 p.Glu773Asp missense_variant 0.11
rpoB 762879 p.Met1025Leu missense_variant 0.1
rpoC 762929 c.-441G>C upstream_gene_variant 0.13
rpoC 763621 c.252C>G synonymous_variant 0.11
rpoC 763633 c.264T>C synonymous_variant 0.1
rpoC 763660 c.291T>G synonymous_variant 0.11
rpoC 763675 c.306C>G synonymous_variant 0.12
rpoC 763696 c.327T>C synonymous_variant 0.12
rpoC 763705 c.336G>C synonymous_variant 0.11
rpoC 764521 c.1152T>C synonymous_variant 0.1
rpoC 764527 c.1158C>G synonymous_variant 0.1
rpoC 764536 c.1167G>C synonymous_variant 0.11
rpoC 764539 c.1170C>G synonymous_variant 0.12
rpoC 764560 c.1191T>C synonymous_variant 0.15
rpoC 764566 c.1197C>G synonymous_variant 0.12
rpoC 764572 c.1203G>C synonymous_variant 0.11
rpoC 764575 c.1206T>G synonymous_variant 0.1
rpoC 764578 c.1209C>G synonymous_variant 0.1
rpoC 764581 c.1212T>C synonymous_variant 0.11
rpoC 764611 c.1242G>C synonymous_variant 0.15
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.16
rpoC 764635 c.1266C>G synonymous_variant 0.15
rpoC 764650 c.1281G>C synonymous_variant 0.15
rpoC 764665 c.1296C>G synonymous_variant 0.15
rpoC 764677 c.1308C>G synonymous_variant 0.17
rpoC 764681 p.Leu438Met missense_variant 0.18
rpoC 764706 p.Leu446Gln missense_variant 0.17
rpoC 764713 c.1344G>C synonymous_variant 0.17
rpoC 764731 c.1362G>C synonymous_variant 0.11
fbiC 1305250 p.Arg774Gly missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472524 n.679G>T non_coding_transcript_exon_variant 0.1
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.12
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.12
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.11
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.11
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.15
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.19
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.19
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.15
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.14
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.11
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.11
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.15
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.15
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.18
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.18
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.18
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.11
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.12
clpC1 4040033 c.672G>C synonymous_variant 0.1
clpC1 4040057 c.648C>T synonymous_variant 0.13
clpC1 4040090 c.615T>C synonymous_variant 0.1