TB-Profiler result

Run: ERR2229366
Summary

Run ID: ERR2229366

Sample name:

Date: 31-03-2023 17:06:43

Number of reads: 1171614

Percentage reads mapped: 94.31

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 0.46 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.25 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
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576288 p.Arg314Leu missense_variant 0.12
rpoB 762218 c.2412T>C synonymous_variant 0.16
rpoB 762233 c.2427G>C synonymous_variant 0.23
rpoB 762236 c.2430G>T synonymous_variant 0.23
rpoB 762245 c.2439G>T synonymous_variant 0.26
rpoB 762254 c.2448T>C synonymous_variant 0.25
rpoB 762257 c.2451C>G synonymous_variant 0.25
rpoC 762899 c.-471G>T upstream_gene_variant 0.16
rpoC 762920 c.-450C>T upstream_gene_variant 0.14
rpoC 762929 c.-441G>C upstream_gene_variant 0.13
rpoC 763534 c.165T>C synonymous_variant 0.13
rpoC 763537 c.168C>G synonymous_variant 0.12
rpoC 763570 c.201G>C synonymous_variant 0.18
rpoC 763573 c.204G>C synonymous_variant 0.17
rpoC 764605 c.1236G>T synonymous_variant 0.17
rpoC 764611 c.1242G>T synonymous_variant 0.17
rpoC 764681 p.Leu438Met missense_variant 0.14
rpoC 765631 c.2262C>T synonymous_variant 0.13
rpoC 766542 p.Gly1058Val missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776187 p.Phe765Ser missense_variant 0.11
mmpL5 777119 p.His454Gln missense_variant 0.19
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.19
mmpS5 778936 c.-31C>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303792 c.864delA frameshift_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471929 n.84C>G non_coding_transcript_exon_variant 0.11
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.11
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.11
rrs 1471936 n.91A>G non_coding_transcript_exon_variant 0.11
rrs 1472085 n.240C>T non_coding_transcript_exon_variant 0.14
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.16
rrs 1472107 n.262A>G non_coding_transcript_exon_variant 0.16
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.16
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.15
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.29
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.28
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.28
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.35
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.33
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.45
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.36
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.25
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.22
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.31
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.31
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.28
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.31
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.52
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.51
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.38
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.36
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.36
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.36
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.41
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.28
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.27
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.27
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.28
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.27
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.27
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.29
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.34
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.33
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.34
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.21
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.3
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.31
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.32
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.28
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.29
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.31
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.42
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.23
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.19
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.27
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.3
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.46
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.39
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.21
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.15
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.12
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.13
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.12
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.16
rrl 1473862 n.205C>T non_coding_transcript_exon_variant 0.19
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.22
rrl 1473887 n.230T>G non_coding_transcript_exon_variant 0.23
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 0.35
rrl 1473922 n.265A>G non_coding_transcript_exon_variant 0.35
rrl 1473923 n.266C>G non_coding_transcript_exon_variant 0.35
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.23
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.2
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.26
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.18
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.24
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.25
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.25
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.28
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.28
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.32
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.32
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.31
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.27
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.27
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.26
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.24
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.25
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.39
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.38
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.31
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.21
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.21
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.23
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.23
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.23
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.22
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.2
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.21
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.45
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.4
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.2
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.2
rrl 1475137 n.1480A>T non_coding_transcript_exon_variant 0.16
rrl 1475170 n.1513A>G non_coding_transcript_exon_variant 0.15
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.13
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.15
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.49
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.33
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.33
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.32
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.44
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.38
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.38
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.42
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.38
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.47
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.5
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.26
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.27
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.25
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.25
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.25
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 0.26
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.24
rrl 1475996 n.2339T>G non_coding_transcript_exon_variant 0.24
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.29
rrl 1476117 n.2460G>A non_coding_transcript_exon_variant 0.27
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.24
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.28
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.33
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.34
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 0.37
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.48
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.49
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.23
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.2
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.31
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.32
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.31
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.31
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.31
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.31
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.45
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.12
rrl 1476564 n.2907G>A non_coding_transcript_exon_variant 0.18
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.23
rrl 1476573 n.2916A>G non_coding_transcript_exon_variant 0.23
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.19
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.19
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
inhA 1674508 p.Met103Val missense_variant 0.25
rpsA 1834069 c.528G>C synonymous_variant 0.3
rpsA 1834273 c.732C>T synonymous_variant 0.15
rpsA 1834286 c.745_746delTCinsAG synonymous_variant 0.15
rpsA 1834294 c.753G>T synonymous_variant 0.15
rpsA 1834486 p.Glu315Asp missense_variant 0.12
rpsA 1834489 c.948T>C synonymous_variant 0.15
rpsA 1834600 c.1059G>C synonymous_variant 0.14
rpsA 1834603 p.Glu354Asp missense_variant 0.13
rpsA 1834606 c.1065C>T synonymous_variant 0.13
rpsA 1834609 c.1068T>C synonymous_variant 0.13
rpsA 1834612 c.1071G>C synonymous_variant 0.13
rpsA 1834619 c.1078T>C synonymous_variant 0.12
rpsA 1834624 c.1083G>C synonymous_variant 0.12
rpsA 1834627 c.1086C>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102927 p.Asp39Val missense_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.26
PPE35 2167967 c.2646A>C synonymous_variant 0.26
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.64
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519067 p.Gly318Ala missense_variant 0.12
kasA 2519143 c.1029G>C synonymous_variant 0.14
folC 2746644 p.Arg319Ser missense_variant 0.18
ribD 2987034 p.Gly66Arg missense_variant 0.22
Rv2752c 3064885 p.Ala436Val missense_variant 0.12
Rv2752c 3065207 p.Thr329Ser missense_variant 0.13
Rv3236c 3612262 c.855A>G synonymous_variant 0.11
alr 3840200 c.1220delA frameshift_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.17
clpC1 4039003 p.Asn568Asp missense_variant 0.14
clpC1 4040587 p.Glu40* stop_gained 0.12
embC 4241102 p.Glu414Lys missense_variant 0.13
embC 4241656 c.1794G>T synonymous_variant 0.12
embA 4242530 c.-703C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245922 p.Gly897Ala missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.19
embB 4246548 p.Pro12Gln missense_variant 0.36
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.36
embB 4246567 c.54G>T synonymous_variant 0.27
aftB 4267901 c.936G>T synonymous_variant 0.33
aftB 4267989 p.Ala283Glu missense_variant 0.14
aftB 4268505 p.Arg111Leu missense_variant 0.12
aftB 4268564 c.273G>A synonymous_variant 0.15
aftB 4269291 c.-455A>T upstream_gene_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