TB-Profiler result

Run: ERR2229399
Summary

Run ID: ERR2229399

Sample name:

Date: 31-03-2023 17:09:36

Number of reads: 772271

Percentage reads mapped: 98.86

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
gyrB 5640 p.Arg134Leu missense_variant 0.13
gyrB 6149 p.Phe304Leu missense_variant 0.15
gyrB 6938 p.Pro567Ser missense_variant 0.2
gyrB 6997 p.Glu586Asp missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8626 p.Arg442His missense_variant 0.12
gyrA 9651 p.Ile784Phe missense_variant 0.2
fgd1 491044 p.Gln88* stop_gained 0.13
fgd1 491210 p.Trp143Leu missense_variant 0.12
mshA 575892 p.Ala182Gly missense_variant 0.14
rpoB 760563 c.757C>A synonymous_variant 0.17
rpoC 764085 p.Asn239Thr missense_variant 0.18
rpoC 764237 p.Leu290Ile missense_variant 0.2
rpoC 764248 c.879C>A synonymous_variant 0.2
rpoC 764852 p.Pro495Thr missense_variant 0.12
rpoC 764882 p.His505Asn missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775716 p.Arg922Gln missense_variant 0.13
mmpL5 775736 c.2745C>G synonymous_variant 0.2
mmpL5 775741 c.2740C>T synonymous_variant 0.13
mmpL5 775943 c.2538C>A synonymous_variant 0.17
mmpL5 776417 c.2064G>C synonymous_variant 0.22
mmpL5 777119 p.His454Gln missense_variant 0.2
mmpL5 777122 c.1359C>T synonymous_variant 0.2
mmpL5 777128 c.1353A>G synonymous_variant 0.18
mmpL5 777630 p.Arg284Leu missense_variant 0.15
rpsL 781380 c.-180C>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781917 p.Lys120Glu missense_variant 0.1
rplC 801155 p.Gly116Val missense_variant 0.22
fbiC 1302884 c.-46delG upstream_gene_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303805 p.Val292Ala missense_variant 0.22
embR 1416691 c.657C>T synonymous_variant 0.13
embR 1417091 p.Ala86Val missense_variant 0.15
embR 1417542 c.-195C>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473019 n.1174G>T non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475342 n.1685C>A non_coding_transcript_exon_variant 0.15
rrl 1476018 n.2361G>A non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
rpsA 1833650 p.Asp37Asn missense_variant 0.17
rpsA 1833934 c.393C>T synonymous_variant 0.12
rpsA 1834798 c.1257C>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918037 p.Arg33Leu missense_variant 0.22
ndh 2101819 p.Lys408Asn missense_variant 0.22
ndh 2102210 p.Ala278Val missense_variant 0.33
ndh 2102610 c.433T>C synonymous_variant 0.14
katG 2154014 p.Ser700Thr missense_variant 0.25
katG 2154850 p.Gly421Val missense_variant 0.18
PPE35 2167865 c.2748G>C synonymous_variant 0.19
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.35
PPE35 2167967 c.2646A>C synonymous_variant 0.35
PPE35 2167973 c.2640A>G synonymous_variant 0.14
PPE35 2168047 p.Leu856Val missense_variant 0.14
PPE35 2168051 p.Val854Ile missense_variant 0.15
PPE35 2168241 p.Ile791Thr missense_variant 0.11
PPE35 2168244 p.Ser790Thr missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168876 p.Phe579Leu missense_variant 0.22
PPE35 2169269 c.1344A>G synonymous_variant 0.24
PPE35 2169272 c.1341C>G synonymous_variant 0.21
PPE35 2169278 c.1335T>C synonymous_variant 0.24
PPE35 2169281 c.1332T>G synonymous_variant 0.22
PPE35 2169287 c.1326T>C synonymous_variant 0.29
PPE35 2169293 c.1320T>C synonymous_variant 0.29
PPE35 2169902 p.Leu237Phe missense_variant 0.3
PPE35 2169910 p.Asn235Tyr missense_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.49
PPE35 2170053 p.Thr187Ser missense_variant 0.53
PPE35 2170147 p.Ser156Ala missense_variant 0.15
PPE35 2170159 p.Ala152Ser missense_variant 0.12
PPE35 2170357 p.Ala86Thr missense_variant 0.12
Rv1979c 2222086 p.Ala360Val missense_variant 0.12
Rv1979c 2222193 c.972G>T synonymous_variant 0.12
Rv1979c 2222225 p.Gly314Ser missense_variant 0.15
Rv1979c 2222810 c.355C>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288845 p.Ile133Val missense_variant 0.11
pncA 2289109 p.Val45Leu missense_variant 0.12
kasA 2518736 p.Ala208Ser missense_variant 0.17
kasA 2518976 p.Gly288Ser missense_variant 0.17
kasA 2519140 c.1026G>C synonymous_variant 0.25
kasA 2519143 c.1029G>C synonymous_variant 0.25
eis 2714713 p.Ala207Glu missense_variant 0.2
eis 2715008 p.Ala109Ser missense_variant 0.29
eis 2715009 p.Ile108Met missense_variant 0.29
eis 2715537 c.-205G>T upstream_gene_variant 0.29
ahpC 2725938 c.-255_-254insA upstream_gene_variant 0.13
pepQ 2860144 p.Val92Gly missense_variant 0.22
ribD 2987336 c.498C>A synonymous_variant 0.25
Rv2752c 3064674 c.1518C>A synonymous_variant 0.14
Rv2752c 3064914 c.1278T>A synonymous_variant 0.15
thyA 3074421 c.51C>A synonymous_variant 0.29
thyA 3074471 p.Val1Leu missense_variant 0.25
fbiD 3339232 p.Val39Leu missense_variant 0.14
fbiD 3339263 p.Ala49Asp missense_variant 0.17
fbiD 3339736 p.Thr207Ala missense_variant 0.17
fprA 3474251 p.Val82Ala missense_variant 0.25
fprA 3475079 p.Gly358Val missense_variant 0.12
Rv3236c 3613132 c.-16G>T upstream_gene_variant 0.29
fbiB 3641914 p.Ala127Asp missense_variant 0.14
alr 3840494 c.927G>T synonymous_variant 0.29
alr 3840535 p.Gly296Trp missense_variant 0.13
alr 3840746 c.675A>G synonymous_variant 0.17
alr 3840773 c.648C>A synonymous_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.17
rpoA 3877961 p.Val183Phe missense_variant 0.2
rpoA 3878422 p.Gly29Val missense_variant 0.13
clpC1 4038568 p.Ile713Val missense_variant 0.13
clpC1 4038773 p.Asp644Glu missense_variant 0.14
clpC1 4038776 p.Glu643Asp missense_variant 0.15
clpC1 4039018 p.Ser563Thr missense_variant 0.14
panD 4044128 p.Gly52Cys missense_variant 0.17
embC 4241370 p.Lys503Arg missense_variant 0.13
embC 4241534 p.Pro558Ala missense_variant 0.15
embC 4241874 p.Leu671Pro missense_variant 0.22
embA 4242520 c.-713G>T upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242914 p.Ala1018Thr missense_variant 0.12
embC 4243047 p.Arg1062Leu missense_variant 0.12
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.17
embC 4243092 p.Leu1077Arg missense_variant 0.2
embC 4243095 p.Gly1078Val missense_variant 0.22
embA 4243099 c.-134G>C upstream_gene_variant 0.22
embA 4243102 c.-131G>T upstream_gene_variant 0.22
embC 4243103 p.Thr1081Pro missense_variant 0.22
embC 4243106 p.Arg1082Ser missense_variant 0.22
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4247512 c.999T>C synonymous_variant 0.17
embB 4247516 p.Asn335Asp missense_variant 0.2
embB 4249774 c.3261C>A synonymous_variant 0.14
aftB 4267005 c.1831delG frameshift_variant 0.12
aftB 4267131 p.Pro569His missense_variant 0.14
aftB 4267862 p.Tyr325* stop_gained 0.18
aftB 4268785 p.Gly18Cys missense_variant 0.18
ubiA 4269511 c.322delG frameshift_variant 0.14
ethA 4328241 c.-768T>C upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 0.96
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0