TB-Profiler result

Run: ERR2514305
Summary

Run ID: ERR2514305

Sample name:

Date: 31-03-2023 20:15:25

Number of reads: 896269

Percentage reads mapped: 99.45

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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.18 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.13 kanamycin, capreomycin, aminoglycosides, amikacin
gid 4408087 c.115delC frameshift_variant 1.0 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
gyrB 6930 p.Ala564Val missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.96
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576398 p.Tyr351Asp missense_variant 0.11
mshA 576403 c.1056C>G synonymous_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767069 p.Thr1234Ser missense_variant 0.2
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 1406088 p.Ala418Asp missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 1.0
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.2
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.14
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.13
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.13
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.13
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.13
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.13
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.13
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.13
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.13
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.13
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.4
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
fabG1 1673560 p.Lys41Leu missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167746 p.Thr956Ser missense_variant 0.11
PPE35 2167760 c.2853G>A synonymous_variant 0.11
PPE35 2167763 p.Ile950Val missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290002 c.-761T>C upstream_gene_variant 0.1
kasA 2519221 c.1107G>A synonymous_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.2
ribD 2987394 p.Gly186Ser missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642098 c.564G>A synonymous_variant 1.0
alr 3840636 p.Pro262Gln missense_variant 1.0
rpoA 3878158 c.329_349delTCGTGCCGCCGGCCGGCGTCA disruptive_inframe_deletion 0.12
rpoA 3878182 p.Asp109Gly missense_variant 0.11
rpoA 3878622 c.-115C>G upstream_gene_variant 1.0
clpC1 4039829 p.Leu292Ile missense_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245883 p.Gly884Asp missense_variant 1.0
embB 4246591 c.78G>A synonymous_variant 0.17
embB 4246757 p.Thr82Ser missense_variant 0.14
ethA 4326230 p.Asp415Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408064 p.Arg47Gly missense_variant 0.11