TB-Profiler result

Run: ERR4814827
Summary

Run ID: ERR4814827

Sample name:

Date: 01-04-2023 13:30:55

Number of reads: 2585754

Percentage reads mapped: 99.04

Strain: lineage3.1.2

Drug-resistance: HR-TB

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.16 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407684 c.518dupA frameshift_variant 1.0 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 490833 c.51G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile 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 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.22
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.19
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.17
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.1
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.18
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.26
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.17
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.21
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.21
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.18
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.14
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.17
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.29
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.25
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.15
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.17
rrl 1476188 n.2531C>T non_coding_transcript_exon_variant 0.25
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.23
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.23
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.23
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.16
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.13
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.11
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.11
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338459 p.Met21Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0