TB-Profiler result

Run: ERR2513862
Summary

Run ID: ERR2513862

Sample name:

Date: 31-03-2023 19:57:17

Number of reads: 543606

Percentage reads mapped: 99.78

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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 2155783 p.Ala110Val missense_variant 0.33 isoniazid
ethA 4326317 p.Tyr386Cys missense_variant 0.2 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
gyrB 5467 c.230_232delTCG disruptive_inframe_deletion 0.18
gyrB 6166 c.927C>T synonymous_variant 1.0
gyrA 6427 c.-875T>C upstream_gene_variant 0.25
gyrB 6767 p.Gly510Ser missense_variant 0.29
gyrA 7293 c.-9G>T upstream_gene_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8623 p.Arg441Leu missense_variant 0.14
gyrA 8681 c.1380C>T synonymous_variant 0.22
gyrA 8924 c.1623C>T synonymous_variant 0.12
gyrA 9233 c.1932C>A synonymous_variant 0.11
gyrA 9649 p.Val783Ala missense_variant 0.13
fgd1 490858 p.Ala26Thr missense_variant 0.33
fgd1 490900 p.His40Asp missense_variant 0.4
mshA 576188 p.Asp281Asn missense_variant 0.33
mshA 576488 p.Val381Leu missense_variant 0.18
ccsA 619984 c.94C>T synonymous_variant 0.22
ccsA 620140 p.Ala84Thr missense_variant 0.25
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoB 760752 p.Leu316Met missense_variant 0.12
rpoB 761061 p.Ala419Thr missense_variant 0.18
rpoB 762166 p.Gly787Val missense_variant 0.11
rpoC 762560 c.-810A>G upstream_gene_variant 0.17
rpoB 762653 p.Trp949Cys missense_variant 0.18
rpoC 763378 c.9C>T synonymous_variant 0.18
rpoC 763842 p.Glu158Gly missense_variant 0.15
rpoC 764959 c.1590G>A synonymous_variant 0.13
rpoC 765084 p.Arg572His missense_variant 0.13
rpoC 765753 p.Asp795Val missense_variant 0.14
rpoC 766590 p.Glu1074Val missense_variant 0.12
rpoC 766824 p.Lys1152Arg missense_variant 0.25
mmpL5 775610 p.Ser957Phe missense_variant 0.14
mmpL5 777180 p.Ala434Glu missense_variant 0.11
mmpS5 778799 p.Gly36Val missense_variant 0.18
rpsL 781682 c.123T>C synonymous_variant 0.12
rplC 800905 p.Pro33Thr missense_variant 0.13
rplC 800932 p.Pro42Thr missense_variant 0.12
rplC 800992 p.Val62Phe missense_variant 0.15
rplC 801248 p.Arg147His missense_variant 0.25
fbiC 1302888 c.-43G>T upstream_gene_variant 0.12
fbiC 1303651 p.Arg241Trp missense_variant 0.18
fbiC 1303673 p.Ala248Asp missense_variant 0.18
fbiC 1303713 c.783C>A synonymous_variant 0.13
fbiC 1303857 c.927C>T synonymous_variant 0.33
fbiC 1304801 p.Arg624Gln missense_variant 0.13
fbiC 1304828 p.Phe633Ser missense_variant 0.11
fbiC 1304990 p.Thr687Lys missense_variant 0.25
Rv1258c 1406139 p.Arg401His missense_variant 0.12
Rv1258c 1406491 p.Arg284Ser missense_variant 0.18
Rv1258c 1406729 c.610_611delCG frameshift_variant 0.18
embR 1417147 c.201C>T synonymous_variant 0.18
atpE 1461054 p.Thr4Ala missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475872 n.2215A>G non_coding_transcript_exon_variant 0.5
rpsA 1833402 c.-140G>T upstream_gene_variant 0.25
rpsA 1833403 c.-139G>A upstream_gene_variant 0.25
rpsA 1833421 c.-121C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917977 p.Arg13Pro missense_variant 0.33
ndh 2101846 c.1197G>A synonymous_variant 0.17
ndh 2102447 p.Gly199Val missense_variant 0.29
ndh 2102565 p.Arg160Trp missense_variant 0.12
katG 2154407 p.Pro569Thr missense_variant 0.13
katG 2155993 p.Pro40Leu missense_variant 0.14
PPE35 2167865 c.2748G>C synonymous_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2169138 p.Thr492Lys missense_variant 0.15
PPE35 2169497 c.1116C>T synonymous_variant 0.12
PPE35 2170286 c.327G>A synonymous_variant 0.18
Rv1979c 2221740 c.1425C>T synonymous_variant 0.11
Rv1979c 2221784 p.Ala461Pro missense_variant 0.12
Rv1979c 2222998 p.Ile56Asn missense_variant 0.18
pncA 2288708 c.534C>T synonymous_variant 0.15
pncA 2288801 c.441A>G synonymous_variant 0.12
pncA 2288905 p.Gly113Arg missense_variant 0.14
pncA 2290221 c.-980C>A upstream_gene_variant 0.22
kasA 2517935 c.-180C>T upstream_gene_variant 0.18
kasA 2518449 p.Val112Ala missense_variant 0.13
kasA 2518486 c.372G>A synonymous_variant 0.12
kasA 2518814 p.Arg234Gly missense_variant 0.22
kasA 2518915 c.801T>C synonymous_variant 0.17
kasA 2518976 p.Gly288Cys missense_variant 0.2
kasA 2519128 c.1014G>C synonymous_variant 0.22
kasA 2519131 c.1017G>C synonymous_variant 0.33
kasA 2519140 c.1026G>C synonymous_variant 0.33
kasA 2519143 c.1029G>C synonymous_variant 0.33
eis 2714130 p.Glu401Asp missense_variant 0.14
ahpC 2726234 p.Gln14His missense_variant 0.11
folC 2746153 c.1446C>T synonymous_variant 0.14
folC 2746829 p.Ala257Val missense_variant 0.17
pepQ 2859440 p.Gly327Ser missense_variant 0.22
pepQ 2859940 p.Arg160Pro missense_variant 1.0
ribD 2986732 c.-107C>T upstream_gene_variant 0.15
ribD 2986856 p.Gln6His missense_variant 0.11
Rv2752c 3065375 p.Ala273Ser missense_variant 0.67
Rv2752c 3066241 c.-50C>T upstream_gene_variant 0.12
thyX 3067320 p.Arg209Gln missense_variant 0.33
thyX 3068052 c.-107C>A upstream_gene_variant 0.22
thyA 3073975 p.Arg166His missense_variant 0.11
thyA 3074343 c.129G>T synonymous_variant 0.13
thyA 3074648 c.-177T>G upstream_gene_variant 0.25
ald 3087203 c.384C>A synonymous_variant 0.18
Rv3083 3448975 p.Arg158Trp missense_variant 0.29
Rv3083 3449502 c.999C>T synonymous_variant 0.11
Rv3083 3449825 p.Ser441Tyr missense_variant 0.12
Rv3083 3449868 c.1365C>T synonymous_variant 0.12
whiB7 3568673 p.Val3Leu missense_variant 0.22
Rv3236c 3612910 p.Leu69Phe missense_variant 0.18
Rv3236c 3613132 c.-16G>T upstream_gene_variant 0.15
fbiA 3640352 c.-191G>A upstream_gene_variant 0.12
fbiA 3640417 c.-126C>T upstream_gene_variant 0.13
fbiB 3640674 c.-861C>T upstream_gene_variant 0.13
fbiB 3641702 c.168C>T synonymous_variant 0.29
fbiB 3641830 p.Leu99Pro missense_variant 0.22
alr 3840458 c.963G>T synonymous_variant 0.2
alr 3840926 p.Asn165Lys missense_variant 0.25
alr 3841230 p.Val64Glu missense_variant 0.14
rpoA 3877961 p.Val183Ile missense_variant 0.18
clpC1 4038379 p.Thr776Ala missense_variant 0.15
clpC1 4038720 p.Leu662Pro missense_variant 0.11
clpC1 4039958 c.747G>T synonymous_variant 0.11
clpC1 4040071 p.Pro212Thr missense_variant 0.25
clpC1 4040178 c.526delC frameshift_variant 0.11
panD 4044072 c.210C>A synonymous_variant 0.17
embC 4240517 p.Asp219Asn missense_variant 0.2
embC 4240746 p.Gly295Asp missense_variant 0.11
embC 4241476 c.1614G>A synonymous_variant 0.13
embC 4241941 c.2079A>C synonymous_variant 0.15
embA 4243463 c.231G>T synonymous_variant 0.14
embA 4244049 p.Asp273Asn missense_variant 0.12
embB 4247383 p.Trp290Cys missense_variant 0.14
embB 4248489 p.Ala659Val missense_variant 0.13
embB 4248719 p.Gly736Arg missense_variant 0.22
embB 4249063 c.2550C>T synonymous_variant 0.14
aftB 4267085 c.1752G>A synonymous_variant 0.12
aftB 4267285 p.Thr518Ala missense_variant 0.13
aftB 4269171 c.-335C>T upstream_gene_variant 1.0
ubiA 4269773 p.Ile21Val missense_variant 0.18
ethA 4326387 p.Ile363Phe missense_variant 0.13
ethA 4326999 p.Gly159Trp missense_variant 0.15
ethR 4327324 c.-225A>G upstream_gene_variant 0.11
ethR 4327414 c.-135G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407542 p.Gly221Arg missense_variant 0.25
gid 4408063 p.Arg47Gln missense_variant 1.0