TB-Profiler result

Run: ERR2229147
Summary

Run ID: ERR2229147

Sample name:

Date: 31-03-2023 16:44:34

Number of reads: 574625

Percentage reads mapped: 90.79

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 0.41 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.29 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 7424 c.123G>A synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.29
mshA 576697 c.1350C>T synonymous_variant 0.22
ccsA 620631 c.741T>A synonymous_variant 0.12
rpoB 761697 p.Asp631Tyr missense_variant 0.17
rpoB 762233 c.2427G>C synonymous_variant 0.15
rpoB 762236 c.2430G>T synonymous_variant 0.15
rpoB 762245 c.2439G>T synonymous_variant 0.15
rpoB 762254 c.2448T>C synonymous_variant 0.14
rpoB 762257 c.2451C>G synonymous_variant 0.12
rpoC 762899 c.-471G>T upstream_gene_variant 0.13
rpoC 762971 c.-399G>C upstream_gene_variant 0.15
rpoC 763534 c.165T>C synonymous_variant 0.29
rpoC 763537 c.168C>G synonymous_variant 0.26
rpoC 763546 c.177A>G synonymous_variant 0.21
rpoC 763570 c.201G>C synonymous_variant 0.35
rpoC 763573 c.204G>C synonymous_variant 0.35
rpoC 763594 c.225C>T synonymous_variant 0.27
rpoC 763622 p.Ala85Ser missense_variant 0.14
rpoC 763627 p.Lys86Asn missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775857 p.Gly875Val missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781679 c.120C>G synonymous_variant 0.12
rpsL 781682 c.123T>G synonymous_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305455 p.Arg842Leu missense_variant 0.17
embR 1417382 c.-35G>A upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.17
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.17
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.37
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.35
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.49
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.38
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.37
rrs 1472344 n.499C>T 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 0.32
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.33
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.25
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.24
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.31
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.3
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.28
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.3
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.27
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.37
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.49
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.42
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.42
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.42
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.36
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.38
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.36
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.48
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.35
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.39
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.36
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.25
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.24
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.3
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.29
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.3
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.34
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.31
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.22
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.41
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.49
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.39
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.34
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.31
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.31
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.31
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.44
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.23
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.23
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.23
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.27
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.46
rrl 1473922 n.265A>G non_coding_transcript_exon_variant 0.43
rrl 1473923 n.266C>G non_coding_transcript_exon_variant 0.43
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474166 n.509G>T non_coding_transcript_exon_variant 0.38
rrl 1474167 n.510T>C non_coding_transcript_exon_variant 0.38
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.38
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.47
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.46
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.5
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.33
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.14
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.12
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.12
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.12
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.11
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.11
rrl 1474287 n.631_649delCCTTTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.13
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.13
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.27
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.41
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.36
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.35
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.41
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.41
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.52
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.5
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.52
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.38
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.38
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.33
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.33
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.33
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.48
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.51
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.5
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.32
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.3
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.31
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.31
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.31
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.31
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.48
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.41
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.44
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.41
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.41
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.54
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.46
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.46
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.46
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.61
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.63
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.42
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.42
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.31
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.35
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.41
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.44
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.39
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.39
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.41
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.48
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.5
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.43
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.27
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.29
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.28
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.48
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.35
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.35
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.35
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.29
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.48
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.52
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.5
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.47
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.47
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.47
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.43
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 0.42
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.42
rrl 1475996 n.2339T>G non_coding_transcript_exon_variant 0.42
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.38
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.38
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.36
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.46
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.36
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.36
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.38
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.38
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.38
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.38
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.49
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.56
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.52
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.52
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.41
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.39
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.39
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.32
rrl 1476288 n.2635_2643delGCACCCCCG non_coding_transcript_exon_variant 0.17
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.17
rrl 1476301 n.2644_2645insCGGTGGCTT non_coding_transcript_exon_variant 0.17
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.16
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.16
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.17
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.17
rrl 1476316 n.2659G>A non_coding_transcript_exon_variant 0.21
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.31
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.21
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.21
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.21
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.23
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.24
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.43
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.39
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.39
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.15
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.19
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.12
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.12
rrl 1476546 n.2889C>T non_coding_transcript_exon_variant 0.12
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.13
rpsA 1834123 c.582C>T synonymous_variant 0.13
rpsA 1834189 c.648G>C synonymous_variant 0.29
rpsA 1834486 p.Glu315Asp missense_variant 0.31
rpsA 1834489 c.948T>C synonymous_variant 0.31
rpsA 1834492 c.951C>T synonymous_variant 0.31
rpsA 1834498 c.957C>T synonymous_variant 0.17
rpsA 1834504 c.963G>C synonymous_variant 0.17
rpsA 1834508 p.Ile323Val missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918579 p.Arg214Trp missense_variant 0.12
ndh 2102599 c.444T>C synonymous_variant 0.15
ndh 2102604 c.439T>C synonymous_variant 0.15
ndh 2102610 c.433T>C synonymous_variant 0.17
ndh 2102875 c.168C>T synonymous_variant 0.14
ndh 2103095 c.-53T>A upstream_gene_variant 0.29
katG 2155251 c.861A>G synonymous_variant 0.15
katG 2155862 p.Met84Leu missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168990 c.1623T>C synonymous_variant 0.15
PPE35 2169269 c.1344A>G synonymous_variant 0.17
PPE35 2169272 c.1341C>G synonymous_variant 0.16
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.28
PPE35 2170053 p.Thr187Ser missense_variant 0.32
PPE35 2170159 p.Ala152Ser missense_variant 0.19
Rv1979c 2222551 p.Tyr205Phe missense_variant 0.12
Rv1979c 2222575 p.Trp197Leu missense_variant 0.15
Rv1979c 2223283 c.-119G>A upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290038 c.-797G>A upstream_gene_variant 0.13
kasA 2518645 c.531G>T synonymous_variant 0.15
kasA 2518864 c.750G>C synonymous_variant 0.29
kasA 2518879 c.765A>G synonymous_variant 0.29
kasA 2518882 c.768C>A synonymous_variant 0.29
eis 2714563 p.Ile257Asn missense_variant 0.17
pepQ 2860107 c.312G>A synonymous_variant 0.17
pepQ 2860597 c.-179A>C upstream_gene_variant 0.18
ribD 2987291 p.Asp151Glu missense_variant 0.18
thyX 3068108 c.-163G>A upstream_gene_variant 0.2
thyA 3074022 p.Phe150Leu missense_variant 0.15
thyA 3074188 p.Gly95Asp missense_variant 0.12
ald 3087918 p.Ala367Ser missense_variant 0.33
fprA 3475361 p.Arg452Gln missense_variant 0.13
Rv3236c 3613002 p.Ala39Ser missense_variant 0.14
fbiA 3641370 c.830delG frameshift_variant 0.14
alr 3840395 p.Cys342* stop_gained 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.15
clpC1 4038691 p.Asp672Asn missense_variant 0.12
embC 4241865 p.Leu668Pro missense_variant 0.18
embC 4242195 p.Gly778Val missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246395 p.Gly1055* stop_gained 0.11
embB 4247028 p.Leu172Arg missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0