TB-Profiler result

Run: SRR11972322
Summary

Run ID: SRR11972322

Sample name:

Date: 03-04-2023 05:37:00

Number of reads: 1275762

Percentage reads mapped: 98.77

Strain: lineage1.1.3.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA RD239 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5117 c.-123G>A upstream_gene_variant 0.67
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491752 p.Phe324Val missense_variant 1.0
mshA 576081 p.Asp245Gly missense_variant 0.17
mshA 576158 p.Val271Ile missense_variant 0.2
ccsA 619819 c.-72G>A upstream_gene_variant 0.15
ccsA 620168 p.Ala93Val missense_variant 0.17
rpoB 761188 p.Arg461His missense_variant 0.14
rpoB 761548 p.Val581Gly missense_variant 0.11
rpoB 761830 p.Gly675Val missense_variant 0.15
rpoB 761886 p.Gln694Glu missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 765370 c.2001G>A synonymous_variant 0.14
rpoC 765635 p.Val756Leu missense_variant 0.12
rpoC 766657 c.3288A>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775986 p.His832Arg missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776741 c.1740C>G synonymous_variant 0.11
mmpL5 776744 c.1737C>G synonymous_variant 0.11
mmpL5 777572 c.909C>T synonymous_variant 1.0
mmpL5 778615 c.-135G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781643 c.84G>A synonymous_variant 0.12
Rv1258c 1406719 c.622T>C synonymous_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834929 p.Ser463Leu missense_variant 0.22
tlyA 1917968 p.Glu10Val missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155748 p.Ala122Thr missense_variant 0.14
katG 2155911 c.201G>A synonymous_variant 1.0
katG 2156449 c.-338G>A upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222716 p.Ala150Asp missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518457 p.Gly115Ser missense_variant 0.12
kasA 2518882 c.768C>T synonymous_variant 0.18
eis 2715168 c.165T>C synonymous_variant 0.1
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746617 p.Ala328Ser missense_variant 0.4
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065526 c.666G>A synonymous_variant 0.17
thyX 3067331 c.615C>T synonymous_variant 0.11
thyA 3073952 c.519delT frameshift_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449805 c.1302C>T synonymous_variant 0.12
Rv3083 3449930 p.Asp476Gly missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475322 p.Arg439His missense_variant 0.25
Rv3236c 3612524 p.Ala198Glu missense_variant 0.12
fbiB 3640914 c.-621C>T upstream_gene_variant 0.17
fbiB 3642022 p.Ala163Val missense_variant 0.12
alr 3840213 p.Arg403His missense_variant 0.12
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
rpoA 3877495 p.Glu338Val missense_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240421 p.Glu187Lys missense_variant 0.14
embC 4240448 p.Gln196Lys missense_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240806 p.Arg315His missense_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 0.86
embC 4241176 c.1314C>T synonymous_variant 0.2
embC 4242074 p.Arg738Trp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243667 c.435C>T synonymous_variant 0.15
embA 4243673 c.441C>T synonymous_variant 0.17
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244268 p.Arg346Trp missense_variant 0.12
embA 4245528 p.Gly766Cys missense_variant 0.2
embA 4245735 p.Ala835Thr missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247598 p.Trp362* stop_gained 0.15
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247827 c.1314C>T synonymous_variant 0.12
embB 4248139 c.1626C>T synonymous_variant 1.0
ubiA 4269338 p.Val166Met missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269521 p.Val105Met missense_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 0.91
ethA 4328043 c.-570G>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407715 p.Lys163Ile missense_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407993 c.210C>T synonymous_variant 0.15
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0