TB-Profiler result

Run: SRR7131168
Summary

Run ID: SRR7131168

Sample name:

Date: 04-04-2023 18:47:39

Number of reads: 1545921

Percentage reads mapped: 99.99

Strain: lineage4.1.2.1

Drug-resistance: Other

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.43 streptomycin
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576468 p.Val374Gly missense_variant 0.4
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761161 p.Leu452Arg missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407079 c.261delC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.36
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.44
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.57
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.4
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.67
rrs 1472350 n.505C>T non_coding_transcript_exon_variant 0.33
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.4
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.29
rrs 1472431 n.586G>A non_coding_transcript_exon_variant 0.29
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.4
rrs 1472958 n.1113A>C non_coding_transcript_exon_variant 0.4
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.4
rrs 1472967 n.1122G>T non_coding_transcript_exon_variant 0.4
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.4
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.4
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.4
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.4
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.4
rrs 1472986 n.1141C>T non_coding_transcript_exon_variant 0.4
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.4
rrs 1472988 n.1143T>G non_coding_transcript_exon_variant 0.4
rrs 1472993 n.1148G>A non_coding_transcript_exon_variant 0.67
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.5
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.5
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.5
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.5
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.67
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.67
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.4
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.4
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.4
rrl 1474926 n.1269C>T non_coding_transcript_exon_variant 0.6
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.4
rrl 1474944 n.1287G>A non_coding_transcript_exon_variant 0.4
rrl 1474948 n.1291C>T non_coding_transcript_exon_variant 0.67
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.15
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
fabG1 1673553 p.Asp38Glu missense_variant 0.19
fabG1 1674107 p.Phe223Tyr missense_variant 0.11
rpsA 1834233 p.Val231Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168006 c.2607C>T synonymous_variant 0.12
PPE35 2168110 p.Thr835Ala missense_variant 0.1
PPE35 2168195 c.2418G>T synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2860112 p.Thr103Ala missense_variant 0.12
pepQ 2860183 p.Val79Gly missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244343 p.Ala371Thr missense_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.25
ethA 4326472 c.1002G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408123 p.Ala27Val missense_variant 1.0