TB-Profiler result

Run: SRR5818683
Summary

Run ID: SRR5818683

Sample name:

Date: 04-04-2023 11:43:57

Number of reads: 1727978

Percentage reads mapped: 97.49

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.99
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9683 c.2382G>T synonymous_variant 0.15
gyrA 9796 p.Gly832Asp missense_variant 0.12
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 764654 p.Val429Ile missense_variant 0.14
rpoC 766674 p.Gly1102Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775911 p.Arg857Leu missense_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777005 c.1476C>A synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781669 p.Val37Ala missense_variant 0.13
rplC 800793 c.-16G>T upstream_gene_variant 0.12
Rv1258c 1407247 p.Trp32Arg missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.14
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.12
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.12
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.12
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.12
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.19
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.14
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.14
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrl 1473527 n.-131G>T upstream_gene_variant 0.12
rrl 1474166 n.509G>A non_coding_transcript_exon_variant 0.13
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.13
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.12
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.11
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.11
rrl 1474317 n.660G>T non_coding_transcript_exon_variant 0.14
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.14
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.21
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.17
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.14
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.14
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.18
rrl 1476194 n.2537A>T non_coding_transcript_exon_variant 0.19
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.19
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.19
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.19
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.17
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.11
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.44
katG 2153970 p.Asp714Glu missense_variant 0.16
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168016 p.Ile866Thr missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.35
PPE35 2170461 p.Gly51Glu missense_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
kasA 2518606 c.492G>C synonymous_variant 0.42
kasA 2518609 p.Met165Ile missense_variant 0.42
kasA 2519077 c.963G>T synonymous_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746307 p.Arg431Pro missense_variant 0.13
folC 2746660 c.938delT frameshift_variant 0.15
folC 2746747 c.852G>A synonymous_variant 0.14
ald 3086668 c.-152G>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087634 p.Gly272Val missense_variant 0.15
ald 3087639 p.Cys274Ser missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612268 c.849C>T synonymous_variant 0.15
fbiB 3640563 c.-972C>T upstream_gene_variant 0.22
rpoA 3877938 p.Asp190Glu missense_variant 0.11
clpC1 4038310 p.Val799Leu missense_variant 0.11
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.38
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.13
embB 4246556 p.Ala15Pro missense_variant 0.13
embB 4246563 p.Leu17Trp missense_variant 0.14
embB 4246567 c.54G>T synonymous_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408174 p.Ala10Val missense_variant 1.0