TB-Profiler result

Run: ERR400319
Summary

Run ID: ERR400319

Sample name:

Date: 01-04-2023 03:43:41

Number of reads: 2335671

Percentage reads mapped: 96.46

Strain: lineage4.8

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 0.67 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 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
mshA 576347 p.Thr334Ala 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 1472558 n.713G>A non_coding_transcript_exon_variant 0.4
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.4
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.5
rrs 1472583 n.738T>C non_coding_transcript_exon_variant 0.5
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.5
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.5
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.5
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.5
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.5
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.5
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.5
rrs 1472685 n.840G>A non_coding_transcript_exon_variant 0.5
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.67
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.67
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.67
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.1
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.27
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.27
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.27
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.27
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.27
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.27
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.33
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.4
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.33
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.29
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.33
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.18
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.17
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.17
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.17
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.17
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.14
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.14
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.14
tlyA 1917821 c.-119C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290132 c.-891C>T upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
rpoA 3878580 c.-74_-73insCAACCCA upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245320 c.2088C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0