TB-Profiler result

Run: ERR4830701
Summary

Run ID: ERR4830701

Sample name:

Date: 01-04-2023 20:24:00

Number of reads: 2509182

Percentage reads mapped: 94.26

Strain: lineage4;lineage3

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 0.92
lineage4 Euro-American LAM;T;S;X;H None 0.08
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 1472362 n.517C>T non_coding_transcript_exon_variant 0.76 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 491742 c.960T>C synonymous_variant 0.97
mshA 576108 p.Ala254Gly missense_variant 0.29
rpoC 762434 c.-936T>G upstream_gene_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417353 c.-6C>G upstream_gene_variant 0.29
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 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472279 n.434T>C non_coding_transcript_exon_variant 0.12
rrl 1473640 n.-17delT upstream_gene_variant 0.12
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.19
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.19
rrl 1474717 n.1060_1061insGCCAG non_coding_transcript_exon_variant 0.16
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.25
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.25
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.2
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.2
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.19
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103202 c.-160C>T upstream_gene_variant 0.98
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.95
PPE35 2169840 p.Gly258Asp missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.96
ahpC 2726105 c.-88G>A upstream_gene_variant 0.92
ribD 2986852 p.Gly5Asp missense_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840533 c.888G>C synonymous_variant 0.93
embC 4242075 p.Arg738Gln missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338471 p.Arg17Ser missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.93