TB-Profiler result

Run: SRR6046433
Summary

Run ID: SRR6046433

Sample name:

Date: 04-04-2023 12:16:43

Number of reads: 944377

Percentage reads mapped: 95.61

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 1472644 n.799C>T non_coding_transcript_exon_variant 0.33 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.25 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
rpoC 767044 c.3675G>C synonymous_variant 0.11
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
fbiC 1303331 p.Arg134Gln missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.33
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.33
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.33
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.25
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.22
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.4
rrl 1474962 n.1305T>C non_coding_transcript_exon_variant 1.0
rrl 1475715 n.2058G>T non_coding_transcript_exon_variant 0.33
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.27
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.33
rrl 1475877 n.2220C>G non_coding_transcript_exon_variant 0.29
rrl 1475878 n.2221T>A non_coding_transcript_exon_variant 0.29
rrl 1475879 n.2222T>C non_coding_transcript_exon_variant 0.29
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.43
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.57
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.29
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.18
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.18
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.18
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.18
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.18
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.18
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.3
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.22
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.4
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.33
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.29
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.29
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.38
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.2
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.25
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.22
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.22
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.21
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.2
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.31
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476574 n.2917A>G non_coding_transcript_exon_variant 0.15
rrl 1476725 n.3068C>A 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 2169308 c.1305C>T synonymous_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 2289799 c.-558G>A 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
fprA 3474893 p.Ser296Cys missense_variant 1.0
fprA 3474971 p.Val322Gly missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242235 c.-998C>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245529 p.Gly766Asp missense_variant 0.11
aftB 4267744 p.Arg365Trp missense_variant 0.13
aftB 4267979 c.857_858insAAAGCCACCACG disruptive_inframe_insertion 0.13
whiB6 4338249 c.273G>A synonymous_variant 0.12
whiB6 4338469 p.Asn18Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0