TB-Profiler result

Run: ERR2229473
Summary

Run ID: ERR2229473

Sample name:

Date: 31-03-2023 17:13:46

Number of reads: 648598

Percentage reads mapped: 99.39

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 9149 c.1848C>A synonymous_variant 0.22
fgd1 491167 p.Phe129Ile missense_variant 0.12
fgd1 491240 p.Asp153Val missense_variant 0.15
fgd1 491377 p.Gly199Cys missense_variant 0.29
ccsA 620167 p.Ala93Ser missense_variant 0.15
ccsA 620752 p.Arg288Trp missense_variant 0.12
rpoB 759819 p.Arg5Cys missense_variant 0.18
rpoB 761152 p.Leu449Gln missense_variant 0.13
rpoB 762422 p.Lys872Asn missense_variant 0.17
rpoB 762724 p.Gly973Val missense_variant 0.12
rpoB 762799 p.Ala998Asp missense_variant 0.25
rpoC 763795 p.Glu142Asp missense_variant 0.15
rpoC 764385 p.Asp339Gly missense_variant 0.22
rpoC 764669 p.Pro434Ala missense_variant 0.25
rpoC 764703 p.Lys445Met missense_variant 0.2
rpoC 765180 p.Gly604Val missense_variant 0.2
rpoC 765215 p.Ala616Thr missense_variant 0.25
rpoC 766320 p.Ala984Gly missense_variant 0.18
rpoC 766778 p.Glu1137Lys missense_variant 0.12
rpoC 766828 c.3459C>T synonymous_variant 0.14
rpoC 766913 p.Asp1182Asn missense_variant 0.25
rpoC 767001 p.Thr1211Lys missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776245 p.Ile746Phe missense_variant 0.18
mmpL5 776262 p.Thr740Asn missense_variant 0.22
mmpL5 776310 p.Gly724Val missense_variant 0.12
mmpL5 777999 p.Leu161Gln missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800913 c.105G>T synonymous_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406388 p.Cys318Tyr missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474373 n.716G>T non_coding_transcript_exon_variant 0.33
rrl 1475069 n.1412G>T non_coding_transcript_exon_variant 0.17
rrl 1475632 n.1975C>T non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
inhA 1674921 p.Lys240Asn missense_variant 0.18
inhA 1674939 c.738G>T synonymous_variant 0.17
rpsA 1834468 c.927A>G synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918138 p.Ala67Ser missense_variant 0.13
PPE35 2168149 p.Pro822Thr missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169107 p.Asp502Glu missense_variant 0.25
PPE35 2169956 c.657T>C synonymous_variant 0.11
PPE35 2169964 p.Leu217Val missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.46
PPE35 2170053 p.Thr187Ser missense_variant 0.43
PPE35 2170147 p.Ser156Ala missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518348 c.234A>T synonymous_variant 0.18
kasA 2518432 p.Asp106Glu missense_variant 0.17
kasA 2518626 p.Cys171Phe missense_variant 0.13
kasA 2519070 p.Asp319Gly missense_variant 0.33
kasA 2519140 c.1026G>C synonymous_variant 0.2
kasA 2519143 c.1029G>C synonymous_variant 0.2
eis 2714536 p.Ser266Ile missense_variant 0.15
ribD 2987382 p.Leu182Ile missense_variant 0.12
Rv2752c 3067015 c.-824T>C upstream_gene_variant 0.17
Rv2752c 3067112 c.-921G>A upstream_gene_variant 0.18
thyX 3067450 p.Gln166Lys missense_variant 0.33
thyA 3074405 p.Gly23Cys missense_variant 0.12
fbiD 3339500 p.Ala128Glu missense_variant 0.14
fprA 3474556 c.552dupA frameshift_variant 0.13
fprA 3475039 p.Gly345Cys missense_variant 0.17
Rv3236c 3612184 p.Phe311Leu missense_variant 0.25
fbiA 3640823 p.Arg94His missense_variant 0.14
fbiA 3641423 p.Asp294Ala missense_variant 0.12
fbiB 3642140 c.607delG frameshift_variant 0.33
fbiB 3642167 c.633G>C synonymous_variant 0.33
alr 3841151 c.270C>T synonymous_variant 0.14
alr 3841165 p.Ala86Ser missense_variant 0.13
alr 3841175 c.246G>T synonymous_variant 0.15
alr 3841275 p.Val49Glu missense_variant 0.12
ddn 3987207 p.Tyr122His missense_variant 0.11
clpC1 4038964 p.Asp581Tyr missense_variant 0.17
clpC1 4039005 p.Ala567Asp missense_variant 0.12
clpC1 4039549 p.Ala386Ser missense_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.27
embC 4241461 c.1599C>T synonymous_variant 0.15
embC 4241544 p.Ala561Asp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243031 c.3173delG frameshift_variant 0.2
embA 4244400 p.Leu390Met missense_variant 0.18
embA 4244842 p.Arg537Gln missense_variant 0.2
embA 4245750 p.Met840Leu missense_variant 0.2
embB 4246587 p.Gly25Val missense_variant 0.33
aftB 4268402 p.Leu145Phe missense_variant 0.22
aftB 4268497 c.340C>A synonymous_variant 0.12
aftB 4268706 p.Gly44Val missense_variant 0.29
aftB 4269192 c.-356C>A upstream_gene_variant 0.17
ubiA 4269331 p.Thr168Asn missense_variant 0.15
ethR 4326655 c.-894G>T upstream_gene_variant 0.17
ethR 4327690 p.Asp48Tyr missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407781 p.Ala141Glu missense_variant 0.13
gid 4407799 p.Val135Glu missense_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0