TB-Profiler result

Run: ERR1750938

Summary

Run ID: ERR1750938

Sample name:

Date: 31-03-2023 15:01:09

Number of reads: 920424

Percentage reads mapped: 83.27

Strain: lineage4.4.1

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
lineage4.4.1 Euro-American (S-type) S;T 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
embB 4247959 p.Met482Ile missense_variant 0.4 ethambutol
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 5940 p.Ser234Asn missense_variant 0.2
gyrB 6066 p.Val276Ala missense_variant 0.29
gyrB 6068 p.Asp277Tyr missense_variant 0.29
gyrA 6712 c.-590G>T upstream_gene_variant 0.2
gyrB 6927 p.Leu563Trp missense_variant 0.27
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7806 p.Arg169Trp missense_variant 0.33
gyrA 8149 p.Phe283Ser missense_variant 0.33
gyrA 8188 c.889delG frameshift_variant 0.4
gyrA 8205 p.Ile302Phe missense_variant 0.4
gyrA 8283 p.Ile328Phe missense_variant 0.33
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.35
fgd1 490962 c.180T>C synonymous_variant 0.33
fgd1 491067 p.Cys95Trp missense_variant 0.29
fgd1 491111 p.Ala110Val missense_variant 0.67
fgd1 491271 c.489C>T synonymous_variant 0.25
mshA 576246 p.Gly300Val missense_variant 0.29
mshA 576751 p.Lys468Asn missense_variant 0.67
ccsA 620072 p.Pro61His missense_variant 0.14
ccsA 620241 c.351C>A synonymous_variant 0.4
ccsA 620748 c.858T>G synonymous_variant 0.43
rpoB 759615 c.-192A>C upstream_gene_variant 0.4
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoB 759843 p.Pro13Ser missense_variant 0.29
rpoB 759887 c.81C>T synonymous_variant 0.33
rpoB 762793 c.2987_2988insA frameshift_variant 0.29
rpoB 763045 p.Gln1080Leu missense_variant 0.4
rpoC 763082 c.-288C>G upstream_gene_variant 0.4
rpoB 763093 p.Val1096Ala missense_variant 0.4
rpoC 763103 c.-267G>C upstream_gene_variant 0.4
rpoC 763115 c.-255T>C upstream_gene_variant 0.5
rpoC 763376 p.Asp3Asn missense_variant 0.67
rpoC 763736 p.Lys123* stop_gained 0.67
rpoC 763950 p.Arg194Leu missense_variant 0.15
rpoC 764003 p.Ala212Ser missense_variant 0.2
rpoC 764038 p.Trp223* stop_gained 0.18
rpoC 764048 c.681delC frameshift_variant 0.2
rpoC 764062 c.693C>A synonymous_variant 0.22
rpoC 764549 p.Pro394Thr missense_variant 0.17
rpoC 766079 p.Arg904Ser missense_variant 0.17
mmpL5 776738 c.1743C>T synonymous_variant 0.67
mmpL5 776741 c.1740C>T synonymous_variant 0.67
mmpL5 776744 c.1737C>G synonymous_variant 0.67
mmpL5 776756 p.Asp575Glu missense_variant 0.67
mmpL5 777250 p.Tyr411Asn missense_variant 0.25
mmpL5 777254 c.1227G>A synonymous_variant 0.22
mmpL5 777258 p.Leu408Gln missense_variant 0.22
mmpL5 777416 c.1065G>T synonymous_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.75
fbiC 1303016 p.Val29Gly missense_variant 0.4
fbiC 1303127 p.Arg66Leu missense_variant 0.25
fbiC 1304627 p.Ala566Glu missense_variant 0.29
fbiC 1305441 c.2511C>T synonymous_variant 0.2
embR 1417542 c.-195C>A upstream_gene_variant 0.5
atpE 1461086 c.42A>G synonymous_variant 0.31
atpE 1461101 c.57T>G synonymous_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.4
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.5
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.4
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.4
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.67
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.5
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.5
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.5
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.5
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.67
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.33
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.33
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.33
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.38
rrs 1472446 n.601_602insTCTGCAA non_coding_transcript_exon_variant 0.38
rrs 1472449 n.606_612delCGGCTTA non_coding_transcript_exon_variant 0.43
rrs 1472459 n.614C>T non_coding_transcript_exon_variant 0.43
rrs 1472462 n.617T>C non_coding_transcript_exon_variant 0.43
rrs 1472463 n.618G>A non_coding_transcript_exon_variant 0.43
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.43
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.38
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.43
rrs 1472497 n.652G>A non_coding_transcript_exon_variant 0.43
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.33
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.29
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.4
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.5
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.33
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.75
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.6
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.8
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.8
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.8
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.6
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.57
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.5
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.43
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.5
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.4
rrl 1474021 n.364A>G non_coding_transcript_exon_variant 1.0
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.5
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.5
rrl 1474720 n.1063C>T non_coding_transcript_exon_variant 0.5
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.5
rrl 1474740 n.1083G>C non_coding_transcript_exon_variant 0.5
rrl 1474747 n.1090C>G non_coding_transcript_exon_variant 0.5
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.5
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.5
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.5
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.5
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.4
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.4
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.4
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.4
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.4
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.5
rrl 1475508 n.1851A>T non_coding_transcript_exon_variant 0.33
rrl 1475748 n.2091G>T non_coding_transcript_exon_variant 0.2
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.22
rrl 1475756 n.2101_2108delACCCGCAA non_coding_transcript_exon_variant 0.25
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.3
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.27
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.31
rrl 1476156 n.2499C>A non_coding_transcript_exon_variant 0.18
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.2
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.25
rrl 1476178 n.2521C>A non_coding_transcript_exon_variant 0.29
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.75
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.6
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.33
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.33
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.71
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.62
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.33
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.33
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.7
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.67
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.33
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.33
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.67
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.67
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.67
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.6
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.4
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.78
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.44
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.45
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.73
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.83
fabG1 1673369 c.-71A>T upstream_gene_variant 0.4
fabG1 1673932 p.Arg165Cys missense_variant 0.4
rpsA 1834451 c.910T>C synonymous_variant 0.4
rpsA 1834456 c.915T>G synonymous_variant 0.4
rpsA 1834468 c.927A>G synonymous_variant 0.4
rpsA 1834483 p.Glu314Asp missense_variant 0.4
rpsA 1834489 c.948T>C synonymous_variant 0.4
rpsA 1834498 c.957C>T synonymous_variant 0.33
rpsA 1834504 c.963G>C synonymous_variant 0.33
rpsA 1834531 c.990C>T synonymous_variant 0.4
rpsA 1834552 c.1011G>T synonymous_variant 0.29
rpsA 1834555 c.1014T>C synonymous_variant 0.29
rpsA 1834564 c.1023C>T synonymous_variant 0.29
rpsA 1834606 c.1065C>T synonymous_variant 0.4
rpsA 1834609 c.1068T>C synonymous_variant 0.33
rpsA 1834619 c.1078T>C synonymous_variant 0.33
rpsA 1834622 c.1081_1083delTCGinsAGC synonymous_variant 0.33
rpsA 1834633 c.1092A>G synonymous_variant 0.33
rpsA 1834639 c.1098T>C synonymous_variant 0.33
rpsA 1834646 p.Tyr369Asn missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918360 p.Pro141Ser missense_variant 0.25
ndh 2101754 p.Thr430Ile missense_variant 0.29
ndh 2102990 p.Val18Ala missense_variant 1.0
ndh 2103227 c.-185T>C upstream_gene_variant 0.25
katG 2154270 c.1842G>A synonymous_variant 1.0
PPE35 2168429 c.2184G>A synonymous_variant 0.18
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169559 c.1052_1053delTG frameshift_variant 0.2
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170304 c.309G>A synonymous_variant 0.15
PPE35 2170585 p.Ile10Phe missense_variant 0.2
PPE35 2170628 c.-16C>T upstream_gene_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288971 p.Glu91Lys missense_variant 0.67
pncA 2289019 p.Gly75Ser missense_variant 0.67
kasA 2518147 c.33C>T synonymous_variant 0.4
kasA 2518678 c.564C>T synonymous_variant 0.4
kasA 2518713 p.Gly200Val missense_variant 0.5
eis 2714844 c.489C>A synonymous_variant 0.2
eis 2714936 p.Pro133Ser missense_variant 0.2
eis 2714955 c.378C>T synonymous_variant 0.2
eis 2715103 p.Leu77Pro missense_variant 0.3
eis 2715229 p.Ala35Val missense_variant 0.67
ahpC 2726265 p.Lys25Gln missense_variant 0.22
ahpC 2726338 p.Val49Gly missense_variant 0.33
ahpC 2726341 p.Val50Gly missense_variant 0.5
ahpC 2726741 c.549G>A synonymous_variant 0.25
folC 2746380 p.Gly407Trp missense_variant 0.4
pepQ 2859524 p.Gly299Cys missense_variant 0.33
pepQ 2859606 c.813G>T synonymous_variant 0.25
pepQ 2859667 c.750_751delTC frameshift_variant 0.25
pepQ 2859736 p.Gly228Glu missense_variant 0.25
Rv2752c 3065724 c.468C>T synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339491 p.Leu125His missense_variant 0.18
Rv3083 3448838 p.Arg112Gln missense_variant 0.18
Rv3083 3448924 p.Gly141Ser missense_variant 0.25
Rv3083 3449382 p.Trp293Cys missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475340 p.Ala445Asp missense_variant 0.43
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3612811 c.306G>T synonymous_variant 0.4
Rv3236c 3613083 p.Gly12Cys missense_variant 0.22
fbiA 3641203 p.Gly221Cys missense_variant 0.67
fbiB 3641418 c.-117C>T upstream_gene_variant 0.4
fbiB 3642169 p.Thr212Lys missense_variant 0.29
fbiB 3642595 p.Pro354Leu missense_variant 0.33
fbiB 3642705 p.Arg391Ser missense_variant 0.18
fbiB 3642732 p.Ser400Thr missense_variant 0.15
rpoA 3878175 c.333G>T synonymous_variant 0.15
rpoA 3878630 c.-124delC upstream_gene_variant 0.25
clpC1 4038223 p.Ala828Ser missense_variant 0.33
clpC1 4038860 c.1845G>C synonymous_variant 0.5
clpC1 4038878 c.1827A>G synonymous_variant 0.6
clpC1 4038890 c.1815G>A synonymous_variant 0.67
clpC1 4038911 c.1794G>T synonymous_variant 0.8
clpC1 4038917 c.1788C>T synonymous_variant 0.8
clpC1 4038923 c.1782A>G synonymous_variant 0.75
clpC1 4038926 c.1779G>T synonymous_variant 0.75
clpC1 4038941 c.1764G>C synonymous_variant 0.75
clpC1 4038944 c.1761C>T synonymous_variant 0.75
clpC1 4038953 c.1752A>G synonymous_variant 0.75
clpC1 4038956 c.1749T>C synonymous_variant 0.75
clpC1 4038965 c.1740T>C synonymous_variant 1.0
clpC1 4038971 c.1734T>C synonymous_variant 1.0
clpC1 4038974 c.1731T>C synonymous_variant 1.0
clpC1 4038980 c.1725C>T synonymous_variant 1.0
clpC1 4038986 p.Asp573Glu missense_variant 1.0
clpC1 4038989 c.1716T>C synonymous_variant 1.0
clpC1 4038997 c.1708T>C synonymous_variant 1.0
clpC1 4039004 c.1701C>G synonymous_variant 1.0
clpC1 4039019 c.1686G>C synonymous_variant 1.0
clpC1 4039022 c.1683A>G synonymous_variant 1.0
clpC1 4039630 p.Leu359Phe missense_variant 0.2
clpC1 4039999 p.Gly236Ser missense_variant 0.25
panD 4043987 p.Arg99Cys missense_variant 0.5
embC 4239973 c.111T>G synonymous_variant 0.5
embC 4240648 c.786C>T synonymous_variant 0.6
embC 4240978 p.Lys372Asn missense_variant 0.33
embA 4242250 c.-983C>A upstream_gene_variant 0.22
embA 4243859 c.627C>T synonymous_variant 0.22
embA 4243861 p.Gly210Asp missense_variant 0.22
embA 4244058 p.Tyr276Asn missense_variant 0.5
embA 4244183 c.951G>A synonymous_variant 0.25
embA 4244222 c.990G>T synonymous_variant 0.18
embA 4244443 p.Arg404Leu missense_variant 0.22
embA 4244450 c.1218C>T synonymous_variant 0.2
embB 4247133 p.Asp207Gly missense_variant 0.22
embB 4247737 c.1224C>T synonymous_variant 0.25
embB 4247816 p.Val435Ile missense_variant 0.2
embB 4247921 p.His470Tyr missense_variant 0.33
embB 4248066 p.Trp518* stop_gained 0.4
embB 4249266 p.Pro918Leu missense_variant 0.29
aftB 4267230 p.Trp536* stop_gained 0.5
ubiA 4268965 p.Ala290Glu missense_variant 0.67
ubiA 4269406 p.Lys143Leu missense_variant 0.5
ubiA 4269646 p.Ser63Ile missense_variant 0.14
ubiA 4269859 c.-26A>C upstream_gene_variant 0.25
ethA 4328216 c.-743C>T upstream_gene_variant 0.25
ethA 4328257 c.-784A>T upstream_gene_variant 0.29
ethA 4328267 c.-794G>T upstream_gene_variant 0.4
ethA 4328328 c.-855C>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0