TB-Profiler result

Run: SRR5535928
Summary

Run ID: SRR5535928

Sample name:

Date: 04-04-2023 10:45:23

Number of reads: 855925

Percentage reads mapped: 99.07

Strain: lineage4.4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.1 Euro-American S;Orphans None 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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8671 p.Lys457Arg missense_variant 0.22
gyrA 8733 p.Ile478Val missense_variant 0.4
gyrA 9091 p.Ala597Asp missense_variant 0.13
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491656 p.Glu292Lys missense_variant 0.29
mshA 576024 p.Ser226* stop_gained 0.18
ccsA 619708 c.-183G>A upstream_gene_variant 0.22
rpoB 759934 p.Glu43Gly missense_variant 0.15
rpoB 762511 p.Ala902Val missense_variant 0.15
rpoB 763281 p.Asn1159Asp missense_variant 0.15
rpoC 764217 p.Asn283Thr missense_variant 0.18
rpoC 764310 p.Leu314Arg missense_variant 0.29
rpoC 764499 p.Ser377Phe missense_variant 0.13
rpoC 765586 c.2217G>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775676 c.2804delA frameshift_variant 0.17
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpR5 779266 p.Phe93Leu missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781508 c.-52G>T upstream_gene_variant 0.13
rplC 800900 p.Ala31Val missense_variant 0.14
fbiC 1304821 p.His631Asn missense_variant 0.14
Rv1258c 1406845 p.Ala166Ser missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472140 n.296delG non_coding_transcript_exon_variant 0.15
rrl 1474815 n.1158A>G non_coding_transcript_exon_variant 0.12
rpsA 1833576 p.Ala12Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
ndh 2103189 c.-147G>A upstream_gene_variant 0.13
katG 2155042 p.Asp357Val missense_variant 0.12
PPE35 2168297 c.2316G>A synonymous_variant 0.33
PPE35 2168323 p.Ile764Val missense_variant 0.29
PPE35 2168414 c.2199G>T synonymous_variant 0.15
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169713 c.900C>A synonymous_variant 0.17
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289455 c.-214G>T upstream_gene_variant 0.14
pncA 2290106 c.-865C>T upstream_gene_variant 0.14
kasA 2518089 c.-26C>A upstream_gene_variant 0.12
eis 2714425 p.Ala303Asp missense_variant 0.18
folC 2746238 p.Pro454Gln missense_variant 0.5
folC 2746356 p.Glu415* stop_gained 0.22
folC 2747025 p.Ala192Thr missense_variant 0.18
pepQ 2860358 p.Ala21Ser missense_variant 0.14
ribD 2987000 c.162C>A synonymous_variant 0.18
Rv2752c 3065863 p.Ala110Asp missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087534 p.Val239Ile missense_variant 0.13
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449433 c.930C>A synonymous_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474096 p.Glu30Asp missense_variant 0.14
fprA 3474473 p.Gly156Val missense_variant 0.14
fprA 3474661 p.Asp219Tyr missense_variant 0.13
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3613021 c.96G>T synonymous_variant 0.18
Rv3236c 3613220 c.-104G>T upstream_gene_variant 0.13
fbiB 3641328 c.-207T>G upstream_gene_variant 0.18
fbiB 3641597 c.63C>A synonymous_variant 0.12
rpoA 3878547 c.-40A>C upstream_gene_variant 0.22
clpC1 4039015 p.Lys564Glu missense_variant 0.13
clpC1 4040083 p.Thr208Pro missense_variant 0.15
clpC1 4040794 c.-90G>T upstream_gene_variant 0.14
embC 4239693 c.-170G>T upstream_gene_variant 0.25
embC 4241445 p.Asp528Gly missense_variant 0.18
embC 4241688 p.Thr609Met missense_variant 0.2
embC 4241723 p.Val621Met missense_variant 0.2
embC 4241739 p.Val626Gly missense_variant 0.22
embC 4241799 p.Phe646Tyr missense_variant 0.12
embC 4242095 p.Ala745Ser missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242779 p.Asn973His missense_variant 0.18
embC 4243033 p.Trp1057Cys missense_variant 0.14
embB 4246905 p.Val131Gly missense_variant 0.14
embB 4247136 p.Thr208Asn missense_variant 0.2
embB 4249200 p.Gln896Arg missense_variant 0.15
aftB 4269024 c.-188G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0