TB-Profiler result

Run: ERR7801204
Summary

Run ID: ERR7801204

Sample name:

Date: 02-04-2023 05:58:47

Number of reads: 684950

Percentage reads mapped: 99.26

Strain: lineage4.3.4.2.1

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
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.98
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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575684 p.Val113Leu missense_variant 0.17
mshA 575687 p.Ala114Ser missense_variant 0.17
ccsA 620330 c.442delC frameshift_variant 0.18
ccsA 620551 p.Asp221Asn missense_variant 0.14
ccsA 620629 p.Gly247Ser missense_variant 0.17
rpoB 760714 p.Ala303Asp missense_variant 0.14
rpoB 760879 p.Pro358Gln missense_variant 0.2
rpoB 760898 c.1092C>A synonymous_variant 0.2
rpoB 761513 p.Glu569Asp missense_variant 0.21
rpoB 762322 p.Gly839Asp missense_variant 0.14
rpoC 762749 c.-621C>A upstream_gene_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767253 p.Pro1295Gln missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777449 c.1032C>A synonymous_variant 0.23
mmpL5 778045 p.Ala146Ser missense_variant 0.22
mmpL5 778657 c.-177C>T upstream_gene_variant 0.18
mmpR5 779073 p.Glu28Asp missense_variant 0.14
mmpR5 779257 p.Arg90Ser missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303845 c.915C>A synonymous_variant 0.2
fbiC 1303859 p.Gly310Val missense_variant 0.18
fbiC 1303974 c.1044C>A synonymous_variant 0.17
fbiC 1304071 p.Thr381Ala missense_variant 0.12
fbiC 1304303 p.Arg458His missense_variant 0.27
Rv1258c 1406816 p.Trp175Cys missense_variant 0.17
Rv1258c 1407023 c.318G>T synonymous_variant 0.17
Rv1258c 1407158 c.183C>A synonymous_variant 0.22
Rv1258c 1407503 c.-163C>A upstream_gene_variant 0.18
embR 1416496 c.852G>T synonymous_variant 0.36
embR 1416829 c.519C>A synonymous_variant 0.2
embR 1416870 p.Glu160* stop_gained 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471671 n.-175G>T upstream_gene_variant 0.17
rrl 1474980 n.1323G>T non_coding_transcript_exon_variant 0.25
rrl 1475114 n.1457C>A non_coding_transcript_exon_variant 0.18
rrl 1475342 n.1685C>A non_coding_transcript_exon_variant 0.29
rrl 1475374 n.1717G>T non_coding_transcript_exon_variant 0.15
fabG1 1673515 p.Gly26Trp missense_variant 0.25
fabG1 1673575 p.His46Asn missense_variant 0.17
inhA 1674239 p.Ser13Ile missense_variant 0.2
inhA 1674278 p.Ala26Glu missense_variant 0.15
inhA 1674953 p.Pro251Leu missense_variant 0.22
rpsA 1833838 c.297G>T synonymous_variant 0.15
rpsA 1834389 p.Pro283Gln missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102550 p.Glu165* stop_gained 0.2
Rv1979c 2222393 p.Ile258Val missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290165 c.-924C>A upstream_gene_variant 0.18
kasA 2519160 p.Ala349Val missense_variant 0.2
eis 2715102 c.231C>A synonymous_variant 0.2
folC 2746230 p.Ala457Ser missense_variant 0.18
folC 2746324 p.Phe425Leu missense_variant 0.25
folC 2746370 p.Arg410Leu missense_variant 0.2
folC 2747011 c.587delC frameshift_variant 0.1
ribD 2986735 c.-104G>T upstream_gene_variant 0.27
ribD 2987363 p.Glu175Asp missense_variant 0.17
ribD 2987499 p.Gly221Cys missense_variant 0.19
Rv2752c 3066208 c.-17C>A upstream_gene_variant 0.23
Rv2752c 3066235 c.-44C>A upstream_gene_variant 0.25
thyX 3067419 p.Pro176His missense_variant 0.19
thyX 3067592 c.354G>T synonymous_variant 0.25
thyX 3067874 c.72C>A synonymous_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074197 p.Pro92Gln missense_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339651 c.534G>T synonymous_variant 0.17
Rv3083 3448584 p.Phe27Leu missense_variant 0.2
Rv3083 3448919 p.Cys139Phe missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612117 p.Gly334Trp missense_variant 0.25
Rv3236c 3612426 p.Ala231Ser missense_variant 0.2
Rv3236c 3612680 p.Arg146Gln missense_variant 0.17
Rv3236c 3612731 p.Ser129Tyr missense_variant 0.17
Rv3236c 3613100 p.Ala6Glu missense_variant 0.17
Rv3236c 3613269 c.-153C>A upstream_gene_variant 0.15
fbiA 3641354 p.Ala271Asp missense_variant 0.13
fbiB 3641370 c.-165C>T upstream_gene_variant 0.19
fbiB 3641942 c.408G>T synonymous_variant 0.2
fbiB 3641992 p.Gly153Val missense_variant 0.2
fbiB 3642039 p.Gly169Cys missense_variant 0.2
fbiB 3642420 p.Arg296* stop_gained 0.13
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840734 p.Phe229Leu missense_variant 0.18
alr 3840889 p.Ala178Thr missense_variant 0.18
rpoA 3877926 c.582G>T synonymous_variant 0.17
rpoA 3878289 c.219C>A synonymous_variant 0.18
ddn 3986967 p.Gln42Lys missense_variant 0.17
ddn 3987014 c.171C>T synonymous_variant 0.14
ddn 3987246 p.Asp135Tyr missense_variant 0.18
ddn 3987252 c.410delA frameshift_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 0.95
clpC1 4038652 p.Gly685Cys missense_variant 0.17
clpC1 4039047 p.Gly553Val missense_variant 0.14
clpC1 4040459 c.245delC frameshift_variant 0.12
embC 4240715 p.His285Asn missense_variant 0.15
embC 4241282 p.Ala474Ser missense_variant 0.14
embC 4241378 p.Val506Leu missense_variant 0.15
embC 4241644 c.1782G>T synonymous_variant 0.22
embC 4241686 c.1824G>T synonymous_variant 0.2
embC 4241710 c.1848G>T synonymous_variant 0.17
embC 4242333 p.Gly824Val missense_variant 0.17
embA 4242634 c.-599G>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243085 p.Leu1075Met missense_variant 0.17
embA 4243702 p.Gly157Val missense_variant 0.18
embA 4244956 p.Gly575Val missense_variant 0.15
embA 4245434 c.2202G>T synonymous_variant 0.2
embA 4245660 p.Ala810Ser missense_variant 0.18
embA 4245765 p.Glu845Tyr missense_variant 0.17
embB 4245791 c.-723C>A upstream_gene_variant 0.17
embB 4247207 p.Ala232Pro missense_variant 1.0
embB 4247773 p.Glu420Asp missense_variant 0.13
embB 4247796 p.Leu428His missense_variant 0.18
embB 4249257 p.Arg915Leu missense_variant 0.17
embB 4249766 p.Arg1085Ser missense_variant 0.2
aftB 4267205 c.1632G>T synonymous_variant 0.2
aftB 4267558 p.Ala427Thr missense_variant 0.2
aftB 4267595 p.Tyr414* stop_gained 0.12
aftB 4268504 c.333G>T synonymous_variant 0.19
ubiA 4269061 p.Ala258Glu missense_variant 0.22
aftB 4269072 c.-236G>A upstream_gene_variant 0.38
ubiA 4269865 c.-32G>A upstream_gene_variant 0.2
ethR 4327904 p.Ala119Val missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
PPE35 2158030 c.-22_*9618del transcript_ablation 1.0