TB-Profiler result

Run: SRR7517718
Summary

Run ID: SRR7517718

Sample name:

Date: 04-04-2023 19:33:43

Number of reads: 1834388

Percentage reads mapped: 94.37

Strain: lineage3

Drug-resistance: HR-TB

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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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 8081 c.780A>G synonymous_variant 1.0
gyrA 8717 c.1416C>A synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491422 p.Gly214Cys missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620456 p.Ala189Val missense_variant 0.3
ccsA 620464 p.Ala192Ser missense_variant 0.22
ccsA 620503 p.Glu205* stop_gained 0.22
ccsA 620766 c.876C>T synonymous_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759760 c.-47C>A upstream_gene_variant 0.29
rpoB 761886 p.Gln694Lys missense_variant 0.21
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764292 p.Ser308* stop_gained 0.29
rpoC 765502 p.Gln711His missense_variant 0.18
rpoC 766324 c.2955C>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776150 p.Met777Ile missense_variant 0.27
mmpL5 779010 c.-530G>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781785 p.Glu76* stop_gained 0.19
fbiC 1304713 p.Gly595Trp missense_variant 0.25
embR 1416577 p.Gln257His missense_variant 0.92
embR 1416636 p.Asp238Tyr missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.14
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrl 1475417 n.1760G>T non_coding_transcript_exon_variant 0.27
rrl 1475961 n.2304C>A non_coding_transcript_exon_variant 0.22
rrl 1476018 n.2361G>A non_coding_transcript_exon_variant 0.22
rrl 1476051 n.2394G>T non_coding_transcript_exon_variant 0.22
rrl 1476149 n.2492C>A non_coding_transcript_exon_variant 0.33
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.17
rrl 1476663 n.3006C>A non_coding_transcript_exon_variant 0.18
inhA 1673868 c.-334C>A upstream_gene_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918533 c.594C>A synonymous_variant 0.2
tlyA 1918566 c.627C>A synonymous_variant 0.2
katG 2154711 p.Leu467Phe missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154991 p.Ser374Tyr missense_variant 0.2
katG 2155666 p.Trp149Leu missense_variant 0.24
PPE35 2167670 p.Phe981Leu missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169552 p.Pro354His missense_variant 0.23
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 2289642 c.-401A>G upstream_gene_variant 0.75
pncA 2290033 c.-792C>A upstream_gene_variant 0.2
kasA 2518070 c.-45C>A upstream_gene_variant 0.29
kasA 2518690 c.576C>A synonymous_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747026 c.573C>A synonymous_variant 0.29
pepQ 2859896 p.Glu175* stop_gained 0.25
pepQ 2859914 p.Glu169* stop_gained 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339507 c.390G>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 1.0
fbiA 3641243 p.Arg234Leu missense_variant 0.21
fbiA 3641440 p.Gly300Trp missense_variant 0.3
rpoA 3878417 p.Gly31Cys missense_variant 0.2
clpC1 4039017 p.Ser563Tyr missense_variant 0.33
clpC1 4040169 p.Thr179Met missense_variant 1.0
clpC1 4040788 c.-84C>A upstream_gene_variant 0.2
embC 4240306 c.444C>A synonymous_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244614 p.Ala461Val missense_variant 0.18
embB 4247932 c.1419C>A synonymous_variant 0.24
aftB 4267623 p.Ser405* stop_gained 0.23
aftB 4269024 c.-188G>A upstream_gene_variant 1.0
ethR 4326970 c.-579G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0