TB-Profiler result

Run: ERR4817489
Summary

Run ID: ERR4817489

Sample name:

Date: 01-04-2023 15:01:17

Number of reads: 524603

Percentage reads mapped: 78.64

Strain: 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 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 0.6 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 1.0
ccsA 620537 p.Val216Gly missense_variant 0.29
ccsA 620748 c.858T>G synonymous_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761330 c.1524G>A synonymous_variant 0.17
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 776018 c.2463G>C synonymous_variant 0.11
mmpL5 776021 c.2460G>C synonymous_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779476 p.Glu163Lys missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407200 c.141G>A synonymous_variant 0.13
embR 1416991 c.357A>G synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.6
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.6
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102401 c.642T>C synonymous_variant 0.11
ndh 2102625 p.Ser140Thr missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.15
PPE35 2170540 c.73C>T synonymous_variant 0.13
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
kasA 2518195 c.81G>A synonymous_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746314 p.Arg429Trp missense_variant 0.14
folC 2746765 p.Gln278His missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448417 c.-87C>G upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612133 c.984C>A synonymous_variant 0.17
fbiB 3642772 p.Asp413Ala missense_variant 0.4
clpC1 4038740 c.1965G>C synonymous_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246934 p.Thr141Pro missense_variant 0.15
embB 4247458 c.945C>T synonymous_variant 0.11
embB 4247462 p.Ser317Ala missense_variant 0.12
embB 4247470 c.957T>C synonymous_variant 0.12
embB 4247472 p.Phe320Tyr missense_variant 0.12
embB 4248760 c.2247G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408070 p.Trp45Gly missense_variant 1.0