TB-Profiler result

Run: ERR2514811
Summary

Run ID: ERR2514811

Sample name:

Date: 31-03-2023 20:34:46

Number of reads: 2018802

Percentage reads mapped: 97.95

Strain: lineage3.1.2

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
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.4 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_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
Rv1258c 1406242 p.Ala367Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.38
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.38
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.43
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.38
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.25
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.22
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.22
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.17
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.44
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.44
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.43
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.33
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.43
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.29
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.43
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.43
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.43
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.38
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.38
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.38
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.38
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.4
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.33
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.33
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.3
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.17
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.18
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.17
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.18
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.2
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.18
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.18
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.25
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.17
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.29
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.14
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.12
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.24
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.25
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.13
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.38
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.36
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.31
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.39
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.12
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.12
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.11
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.11
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A 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
pncA 2289801 c.-560C>T 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
aftB 4268594 c.243C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0