TB-Profiler result

Run: ERR1950054
Summary

Run ID: ERR1950054

Sample name:

Date: 31-03-2023 15:38:39

Number of reads: 400259

Percentage reads mapped: 97.51

Strain: lineage4

Drug-resistance: Sensitive

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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
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
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
gyrB 5494 c.255G>T synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7666 p.Asp122Ala missense_variant 0.33
gyrA 9121 p.Arg607His missense_variant 0.13
fgd1 491174 p.Arg131Leu missense_variant 0.22
fgd1 491588 p.Glu269Gly missense_variant 0.29
rpoB 759694 c.-113_-112insG upstream_gene_variant 0.22
rpoB 761337 p.Arg511Cys missense_variant 0.14
rpoC 763944 p.Asp192Gly missense_variant 0.11
rpoC 765926 p.Thr853Ala missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776118 p.Phe788Tyr missense_variant 0.2
mmpL5 776407 p.Pro692Ser missense_variant 0.2
mmpL5 776734 p.Ser583Gly missense_variant 0.22
mmpR5 778208 c.-782C>T upstream_gene_variant 0.12
mmpL5 778398 p.Ile28Thr missense_variant 0.13
mmpL5 778426 p.Ala19Ser missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781624 p.Ala22Glu missense_variant 0.12
fbiC 1302827 c.-104A>G upstream_gene_variant 0.11
fbiC 1302857 c.-74G>A upstream_gene_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304753 p.Glu608Gly missense_variant 0.15
Rv1258c 1406915 c.426C>A synonymous_variant 0.15
atpE 1461255 p.Met71Val missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472350 n.505C>T non_coding_transcript_exon_variant 0.12
rrs 1472885 n.1042delG non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476704 n.3053delC non_coding_transcript_exon_variant 0.13
tlyA 1917825 c.-115G>T upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156569 c.-458C>T upstream_gene_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169158 p.Leu485Phe missense_variant 0.15
PPE35 2170326 p.Glu96Ala missense_variant 0.29
PPE35 2170347 c.265dupC frameshift_variant 0.29
Rv1979c 2222135 p.Asn344Tyr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519015 p.Ser301Pro missense_variant 0.29
ahpC 2726331 p.Trp47Arg missense_variant 0.14
folC 2746446 p.Lys385Glu missense_variant 0.29
folC 2746453 c.1146G>A synonymous_variant 0.29
pepQ 2859471 c.948A>G synonymous_variant 0.4
Rv2752c 3064538 p.Val552Met missense_variant 0.4
Rv2752c 3065042 p.Leu384Ile missense_variant 0.11
fbiD 3339010 c.-108T>C upstream_gene_variant 0.12
Rv3083 3448307 c.-197T>G upstream_gene_variant 0.25
fprA 3474051 c.45G>A synonymous_variant 0.13
whiB7 3568582 p.Pro33Gln missense_variant 0.13
fbiA 3640394 c.-149G>A upstream_gene_variant 0.17
fbiA 3640527 c.-16G>C upstream_gene_variant 0.25
alr 3841476 c.-56G>T upstream_gene_variant 0.11
rpoA 3878328 c.180G>T synonymous_variant 0.18
clpC1 4038599 p.Lys702Asn missense_variant 0.13
clpC1 4038730 p.Asn659Asp missense_variant 0.13
embC 4241034 p.Pro391Leu missense_variant 0.15
embC 4241648 p.Leu596Val missense_variant 0.2
embA 4242550 c.-683C>T upstream_gene_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243864 p.Val211Gly missense_variant 0.4
embA 4244416 p.Leu395Ser missense_variant 0.17
embA 4245148 p.Pro639Leu missense_variant 0.11
embB 4246181 c.-333C>G upstream_gene_variant 0.11
embB 4248278 p.Pro589Thr missense_variant 0.15
embB 4248329 p.Met606Leu missense_variant 0.13
embB 4248597 p.Glu695Val missense_variant 0.2
aftB 4267713 p.Leu375Arg missense_variant 0.22
aftB 4268895 c.-59T>G upstream_gene_variant 0.25
ubiA 4268961 p.Trp291Cys missense_variant 0.22
ethA 4327548 c.-75C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0