TB-Profiler result

Run: ERR2228965
Summary

Run ID: ERR2228965

Sample name:

Date: 31-03-2023 16:28:32

Number of reads: 299839

Percentage reads mapped: 60.78

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 0.74 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.92 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
gyrB 6077 p.Gly280Ser missense_variant 0.29
gyrB 6468 p.Ala410Gly missense_variant 0.29
gyrB 7085 p.Met616Val missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7409 c.108C>T synonymous_variant 0.2
gyrA 8870 c.1569G>T synonymous_variant 0.15
fgd1 491295 c.513C>A synonymous_variant 0.22
mshA 575505 p.His53Arg missense_variant 0.17
mshA 576143 p.Arg266Cys missense_variant 0.29
ccsA 619817 c.-74C>A upstream_gene_variant 0.4
ccsA 619972 p.Ala28Thr missense_variant 0.29
ccsA 620052 c.162G>A synonymous_variant 0.25
rpoB 761549 c.1743G>A synonymous_variant 0.25
rpoB 762218 c.2412T>C synonymous_variant 0.22
rpoB 762233 c.2427G>C synonymous_variant 0.22
rpoB 762236 c.2430G>T synonymous_variant 0.22
rpoB 762245 c.2439G>T synonymous_variant 0.2
rpoB 762254 c.2448T>C synonymous_variant 0.2
rpoB 762257 c.2451C>G synonymous_variant 0.18
rpoB 762616 p.Gly937Asp missense_variant 1.0
rpoC 762899 c.-471G>T upstream_gene_variant 0.27
rpoC 762920 c.-450C>T upstream_gene_variant 0.23
rpoC 762929 c.-441G>C upstream_gene_variant 0.17
rpoC 762959 c.-411G>T upstream_gene_variant 0.17
rpoC 762971 c.-399G>C upstream_gene_variant 0.17
rpoC 762983 c.-387C>T upstream_gene_variant 0.17
rpoC 762989 c.-381G>A upstream_gene_variant 0.18
rpoC 762995 c.-375G>T upstream_gene_variant 0.14
rpoC 763534 c.165T>C synonymous_variant 0.4
rpoC 763537 c.168C>G synonymous_variant 0.5
rpoC 763546 c.177A>G synonymous_variant 0.42
rpoC 763570 c.201G>C synonymous_variant 0.69
rpoC 763573 c.204G>C synonymous_variant 0.69
rpoC 763594 c.225C>T synonymous_variant 0.58
rpoC 763622 p.Ala85Ser missense_variant 0.27
rpoC 763627 p.Lys86Asn missense_variant 0.27
rpoC 763882 p.Glu171Asp missense_variant 0.18
rpoC 763886 p.Arg173Trp missense_variant 0.18
rpoC 764692 c.1323C>T synonymous_variant 0.13
rpoC 764715 c.1348delG frameshift_variant 0.13
rpoC 764731 c.1362G>T synonymous_variant 0.12
rpoC 764737 c.1368G>C synonymous_variant 0.12
rpoC 764868 p.Arg500His missense_variant 0.13
rpoC 765152 p.Asp595Asn missense_variant 0.5
rpoC 766808 p.Val1147Met missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775938 p.Ala848Val missense_variant 0.29
mmpL5 776780 c.1701G>A synonymous_variant 0.25
mmpL5 776969 p.Gln504His missense_variant 0.25
mmpL5 777937 p.Val182Ile missense_variant 0.12
mmpL5 778448 c.32delG frameshift_variant 0.2
mmpR5 779094 p.Leu35Phe missense_variant 0.22
mmpL5 779169 c.-689C>T upstream_gene_variant 0.33
mmpL5 779463 c.-983G>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781781 c.222G>C synonymous_variant 0.4
rpsL 781793 c.234G>C synonymous_variant 0.4
rplC 800775 c.-34G>A upstream_gene_variant 0.15
rplC 800905 p.Pro33Thr missense_variant 0.25
rplC 800953 p.Ala49Thr missense_variant 0.33
rplC 801170 p.Lys121Arg missense_variant 0.18
fbiC 1302802 c.-129G>T upstream_gene_variant 0.22
fbiC 1303014 c.84G>A synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406209 p.Ala378Ser missense_variant 0.15
Rv1258c 1407152 c.189C>A synonymous_variant 0.17
Rv1258c 1407210 p.Ala44Asp missense_variant 0.18
embR 1416399 p.Asp317His missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.45
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.58
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.38
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.29
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.5
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.5
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.5
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.5
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.5
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.5
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 1.0
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.5
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.5
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.6
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.78
rrs 1472744 n.899A>T non_coding_transcript_exon_variant 0.13
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.69
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.64
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.33
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.19
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.19
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.37
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.37
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.43
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.45
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.36
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.35
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.28
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.28
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.31
rrs 1473094 n.1249T>G non_coding_transcript_exon_variant 0.33
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.31
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.31
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.31
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.31
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.28
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.28
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.28
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.28
rrs 1473122 n.1277T>G non_coding_transcript_exon_variant 0.28
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.28
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.38
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.48
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.48
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.54
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.74
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.72
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.75
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.86
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.86
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.92
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.92
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.91
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.91
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.91
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.91
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.56
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.5
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.5
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.5
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 1.0
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 1.0
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 1.0
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 1.0
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 1.0
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 1.0
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.8
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.8
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.8
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.5
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.5
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.5
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.64
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.69
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.33
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.33
rrl 1475137 n.1480A>T non_coding_transcript_exon_variant 0.67
rrl 1475170 n.1513A>G non_coding_transcript_exon_variant 0.5
rrl 1475171 n.1514C>T non_coding_transcript_exon_variant 0.5
rrl 1475175 n.1518G>C non_coding_transcript_exon_variant 0.5
rrl 1475176 n.1519G>A non_coding_transcript_exon_variant 0.5
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.38
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.86
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.83
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.75
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.75
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.43
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.6
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.64
rrl 1475861 n.2204A>G non_coding_transcript_exon_variant 0.25
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.44
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.44
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.44
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.44
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.4
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.4
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.4
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.45
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.42
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.55
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.55
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.5
rrl 1476117 n.2460G>A non_coding_transcript_exon_variant 0.5
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.75
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.75
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.8
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.83
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.71
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.71
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.83
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.83
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.83
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.83
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.89
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.75
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.75
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.53
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.5
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.5
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.53
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.56
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.6
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.73
rrl 1476493 n.2836A>C non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.6
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.33
fabG1 1673803 p.Arg122Trp missense_variant 0.15
fabG1 1673870 p.Ser144Ile missense_variant 0.15
inhA 1674537 c.336C>A synonymous_variant 0.4
inhA 1674730 p.Arg177Ser missense_variant 0.22
inhA 1674765 c.564C>A synonymous_variant 0.22
rpsA 1833397 c.-145G>T upstream_gene_variant 0.33
rpsA 1833599 p.Glu20* stop_gained 0.13
rpsA 1834000 c.459G>T synonymous_variant 0.33
rpsA 1834012 c.471G>A synonymous_variant 0.27
rpsA 1834015 c.474G>C synonymous_variant 0.27
rpsA 1834018 c.477C>T synonymous_variant 0.27
rpsA 1834024 c.483G>C synonymous_variant 0.25
rpsA 1834034 p.Ile165Val missense_variant 0.21
rpsA 1834039 c.498C>T synonymous_variant 0.21
rpsA 1834040 p.Lys167Gln missense_variant 0.21
rpsA 1834069 c.528G>C synonymous_variant 0.29
rpsA 1834099 c.558C>G synonymous_variant 0.33
rpsA 1834828 c.1287C>A synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918319 p.Arg127Gln missense_variant 0.4
ndh 2102228 p.Ala272Asp missense_variant 0.2
katG 2155852 p.Ser87Leu missense_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169430 p.Gly395Ser missense_variant 0.17
PPE35 2170630 c.-18C>A upstream_gene_variant 0.29
Rv1979c 2221879 p.Ala429Val missense_variant 0.14
Rv1979c 2222132 p.Gln345Lys missense_variant 0.18
Rv1979c 2222192 p.Arg325Trp missense_variant 0.22
Rv1979c 2222308 p.Asp286Val missense_variant 0.2
Rv1979c 2222675 p.Gly164* stop_gained 0.22
Rv1979c 2222716 p.Ala150Asp missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289584 c.-343A>T upstream_gene_variant 0.22
kasA 2518022 c.-93C>G upstream_gene_variant 0.4
kasA 2519317 c.1203G>A synonymous_variant 0.15
eis 2714802 c.531G>T synonymous_variant 0.17
eis 2714873 p.Pro154Ser missense_variant 0.17
eis 2715015 c.318C>T synonymous_variant 0.33
folC 2746586 p.Arg338Leu missense_variant 0.2
folC 2746831 c.768G>T synonymous_variant 0.25
folC 2747196 p.Asp135Tyr missense_variant 0.67
pepQ 2859364 p.Pro352His missense_variant 0.22
pepQ 2859422 p.Arg333Cys missense_variant 0.4
pepQ 2860469 c.-51C>A upstream_gene_variant 0.22
ribD 2987361 p.Glu175* stop_gained 0.25
Rv2752c 3065519 p.Leu225Ile missense_variant 0.33
Rv2752c 3065887 c.304delG frameshift_variant 0.29
thyX 3067383 p.Asn188Ile missense_variant 0.33
thyX 3067623 p.Tyr108Cys missense_variant 0.22
thyX 3067904 c.42G>A synonymous_variant 0.33
thyA 3073784 p.Leu230Ile missense_variant 0.22
thyA 3074630 c.-159C>A upstream_gene_variant 0.17
ald 3087131 c.312C>T synonymous_variant 0.2
ald 3087635 c.816C>A synonymous_variant 0.5
fbiD 3339499 p.Ala128Ser missense_variant 0.22
fprA 3474874 p.Gly290Cys missense_variant 0.29
fprA 3474877 p.Arg291Cys missense_variant 0.29
fprA 3475184 p.Ala393Asp missense_variant 0.5
whiB7 3568870 c.-191G>A upstream_gene_variant 0.15
Rv3236c 3612056 p.Leu354Ser missense_variant 0.2
fbiA 3640571 p.Val10Asp missense_variant 0.33
fbiA 3640810 p.Gln90Glu missense_variant 0.2
fbiA 3640855 p.Gly105Trp missense_variant 0.5
fbiB 3642579 p.Ile349Leu missense_variant 0.18
alr 3840763 p.Ala220Ser missense_variant 0.2
alr 3841501 c.-81G>T upstream_gene_variant 0.17
rpoA 3878246 p.Glu88* stop_gained 0.17
ddn 3986948 p.Glu35Asp missense_variant 0.22
ddn 3987276 p.Pro145Ala missense_variant 0.2
clpC1 4038460 c.2245C>T synonymous_variant 0.22
clpC1 4038910 p.Pro599Thr missense_variant 0.15
clpC1 4039672 p.Val345Met missense_variant 0.22
clpC1 4039685 c.1020C>T synonymous_variant 0.22
clpC1 4039694 c.1011G>C synonymous_variant 0.2
clpC1 4039718 c.987C>T synonymous_variant 0.18
clpC1 4040382 p.Ile108Asn missense_variant 0.29
panD 4044209 p.Ser25Thr missense_variant 1.0
embC 4239727 c.-136A>T upstream_gene_variant 0.12
embC 4240490 p.Pro210Thr missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244634 p.Val468Met missense_variant 0.67
embA 4244739 p.Tyr503Asn missense_variant 0.18
embA 4244910 p.Leu560Met missense_variant 0.67
embA 4245163 c.1934delC frameshift_variant 0.25
embA 4245569 p.Glu779Asp missense_variant 0.33
embA 4245673 p.Gly814Val missense_variant 0.29
embA 4246477 p.Pro1082His missense_variant 0.22
embB 4246762 c.249G>T synonymous_variant 0.12
embB 4248163 c.1650G>A synonymous_variant 0.14
embB 4248172 c.1659G>A synonymous_variant 0.15
embB 4248834 p.Trp774Leu missense_variant 0.29
embB 4249606 c.3093C>A synonymous_variant 0.67
aftB 4268365 p.Trp158Arg missense_variant 0.14
aftB 4268400 p.Ala146Gly missense_variant 0.11
aftB 4268413 p.Gly142Trp missense_variant 0.14
ethA 4326315 p.Thr387Ala missense_variant 0.18
ethA 4326380 p.Thr365Met missense_variant 0.25
ethA 4327394 p.Cys27Phe missense_variant 0.33
ethA 4328064 c.-591G>T upstream_gene_variant 0.22
ethA 4328221 c.-748A>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338625 c.-104C>A upstream_gene_variant 0.12
gid 4407950 p.Asp85Tyr missense_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0