TB-Profiler result

Run: SRR1173182
Summary

Run ID: SRR1173182

Sample name:

Date: 03-04-2023 03:18:36

Number of reads: 1975824

Percentage reads mapped: 93.77

Strain: lineage4.6.1.1

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.1 Euro-American T2-Uganda RD724 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.14 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.22 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.15
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.14
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.17
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.16
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.14
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.1
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.11
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.12
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.23
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.13
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.14
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.12
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.12
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.12
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.16
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.12
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.12
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.12
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.12
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.11
rrl 1474905 n.1248T>A non_coding_transcript_exon_variant 0.18
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.1
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.17
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.17
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.17
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.16
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.16
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.12
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.11
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.13
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.14
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.11
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.11
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.29
Rv1979c 2223293 c.-129A>G 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
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0