TB-Profiler result

Run: ERR2229436

Summary

Run ID: ERR2229436

Sample name:

Date: 31-03-2023 17:11:24

Number of reads: 724716

Percentage reads mapped: 95.46

Strain: lineage4.8

Drug-resistance: Other


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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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.28 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.26 kanamycin, capreomycin, aminoglycosides, amikacin
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 8616 p.Gln439Lys missense_variant 0.14
mshA 575606 p.Glu87Lys missense_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576556 p.Asp403Glu missense_variant 0.18
mshA 576777 p.Gly477Val missense_variant 0.25
rpoB 762197 c.2391C>T synonymous_variant 0.18
rpoB 762209 c.2403C>T synonymous_variant 0.17
rpoB 762218 c.2412T>C synonymous_variant 0.18
rpoC 762899 c.-471G>T upstream_gene_variant 0.14
rpoC 762929 c.-441G>C upstream_gene_variant 0.13
rpoC 763820 p.Leu151Phe missense_variant 0.15
rpoC 766024 c.2655C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 c.2755C>T synonymous_variant 0.14
mmpL5 775727 c.2754C>G synonymous_variant 0.14
mmpL5 775736 c.2745C>G synonymous_variant 0.14
mmpL5 775741 c.2740C>T synonymous_variant 0.14
mmpL5 775742 c.2739C>T synonymous_variant 0.14
mmpL5 775981 p.Leu834Met missense_variant 0.15
mmpL5 775987 p.His832Tyr missense_variant 0.17
mmpL5 775990 c.2491C>T synonymous_variant 0.17
mmpL5 776080 p.Ala801Ser missense_variant 0.22
mmpL5 776081 c.2400G>A synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800753 c.-56C>A upstream_gene_variant 0.13
fbiC 1303597 p.Phe223Leu missense_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406303 c.1038C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.19
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.19
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.19
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.31
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.32
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.15
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.18
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.29
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.29
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.15
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.2
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.24
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.31
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.27
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.25
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.27
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.27
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.55
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.44
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.21
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.22
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.21
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.21
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.2
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.21
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.24
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.22
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.13
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.16
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.19
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.25
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.19
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.22
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.22
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.16
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.22
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.22
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.24
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.23
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.23
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.26
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.15
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.15
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.16
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.16
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.2
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.21
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.21
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.21
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.21
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.15
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.15
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.17
rrl 1473922 n.265A>G non_coding_transcript_exon_variant 0.16
rrl 1473923 n.266C>G non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474166 n.509G>T non_coding_transcript_exon_variant 0.22
rrl 1474167 n.510T>C non_coding_transcript_exon_variant 0.19
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.25
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.26
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.21
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.2
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.17
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.24
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.22
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.22
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.22
rrl 1474269 n.612C>A non_coding_transcript_exon_variant 0.21
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.21
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.16
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.14
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.16
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.24
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.26
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.26
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.25
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.19
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.21
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.21
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.19
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.21
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.18
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.19
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.33
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.22
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.11
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.12
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.2
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.16
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.16
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.16
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.3
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.32
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.34
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.34
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.13
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.38
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.23
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.21
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.22
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.21
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.2
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.18
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.17
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.33
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.25
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.23
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.2
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.3
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.17
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.17
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.17
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.21
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.24
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.27
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.19
rrl 1475996 n.2339T>G non_coding_transcript_exon_variant 0.11
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.14
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.16
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.19
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.19
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.17
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.17
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.22
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.27
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.13
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.3
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
inhA 1674489 c.290delT frameshift_variant 0.25
tlyA 1917791 c.-149C>T upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918148 p.Leu70Pro missense_variant 0.17
tlyA 1918292 p.Leu118Gln missense_variant 0.2
PPE35 2167745 p.Thr956Arg missense_variant 0.4
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169337 p.Asp426His missense_variant 0.12
PPE35 2169732 p.Asn294Ser missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.45
PPE35 2170271 c.342T>C synonymous_variant 0.12
PPE35 2170280 c.333C>G synonymous_variant 0.22
PPE35 2170298 c.315A>G synonymous_variant 0.11
PPE35 2170371 p.Thr81Val missense_variant 0.17
PPE35 2170385 c.228G>T synonymous_variant 0.18
PPE35 2170392 p.Gly74Ala missense_variant 0.16
PPE35 2170400 c.213G>C synonymous_variant 0.22
PPE35 2170415 c.198A>G synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289757 c.-516C>T upstream_gene_variant 0.18
pncA 2289823 c.-582T>C upstream_gene_variant 0.15
pncA 2290205 c.-964T>C upstream_gene_variant 0.25
pncA 2290207 c.-966G>T upstream_gene_variant 0.25
ahpC 2725938 c.-255_-254insA upstream_gene_variant 0.29
folC 2747689 c.-91C>A upstream_gene_variant 0.18
pepQ 2859967 c.451delG frameshift_variant 0.22
Rv2752c 3066069 p.Leu41Phe missense_variant 0.2
fbiD 3339238 p.Ala41Ser missense_variant 0.15
fbiD 3339365 p.Pro83Leu missense_variant 0.2
fprA 3474158 p.Ser51Tyr missense_variant 0.2
fprA 3475330 p.Val442Phe missense_variant 0.17
Rv3236c 3612523 c.594G>A synonymous_variant 0.17
Rv3236c 3612866 p.Ser84Asn missense_variant 0.22
fbiA 3641280 p.Ile246Met missense_variant 0.12
ddn 3986938 p.Asn32Ile missense_variant 0.17
clpC1 4038501 p.Ile735Thr missense_variant 1.0
clpC1 4039042 p.Ser555Thr missense_variant 0.17
clpC1 4039161 p.His515Gly missense_variant 0.12
clpC1 4039169 p.Glu512Asp missense_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.13
clpC1 4039654 p.Thr351Ser missense_variant 0.13
embC 4240274 p.Pro138Thr missense_variant 0.14
embC 4240614 p.Leu251Pro missense_variant 0.11
embC 4240636 c.774G>A synonymous_variant 0.12
embC 4241013 p.Met384Thr missense_variant 0.12
embC 4241945 p.Arg695Trp missense_variant 0.15
embC 4241995 c.2133C>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.4
embA 4242847 c.-386C>G upstream_gene_variant 0.11
embA 4244821 p.Gly530Val missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.44
embB 4246548 p.Pro12Gln missense_variant 0.44
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4248908 p.Ala799Thr missense_variant 0.12
embB 4249211 p.Leu900Phe missense_variant 0.15
ethR 4328102 c.555_560delGTCATT disruptive_inframe_deletion 0.13
ethR 4328111 p.Ala188Gly missense_variant 0.12
ethR 4328117 p.Glu190Val missense_variant 0.12
whiB6 4338276 c.246C>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0