TB-Profiler result

Run: SRR2100537
Summary

Run ID: SRR2100537

Sample name:

Date: 19-10-2023 16:08:13

Number of reads: 2511702

Percentage reads mapped: 94.24

Strain: lineage3

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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
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 0.98
rpoC 762434 c.-936T>G upstream_gene_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766582 c.3213C>A synonymous_variant 0.98
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.52
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.4
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.44
rrs 1472675 n.830_838delTCCTTCCTTinsCCTTCCAC non_coding_transcript_exon_variant 0.35
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.36
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.38
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.21
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.36
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.24
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.24
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.27
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.25
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.25
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.26
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.26
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.26
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.22
rrs 1473282 n.1437C>T non_coding_transcript_exon_variant 0.19
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.2
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.33
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.36
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.36
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.34
rrl 1475113 n.1456C>T non_coding_transcript_exon_variant 0.38
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.38
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.38
rrl 1475144 n.1487G>A non_coding_transcript_exon_variant 0.31
rrl 1475163 n.1506T>C non_coding_transcript_exon_variant 0.27
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.27
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.29
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.32
rrl 1475481 n.1824C>T non_coding_transcript_exon_variant 0.32
rrl 1475482 n.1825A>T non_coding_transcript_exon_variant 0.33
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.28
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.31
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.26
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.16
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.3
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.23
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.21
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.21
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.21
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.22
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.26
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.98
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714664 p.Tyr223* stop_gained 0.97
ahpC 2726105 c.-88G>A upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408340 c.-138C>T upstream_gene_variant 0.94