TB-Profiler result

Run: ERR4815816
Summary

Run ID: ERR4815816

Sample name:

Date: 01-04-2023 14:04:48

Number of reads: 3257136

Percentage reads mapped: 92.23

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 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 0.63 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.38 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 7451 c.150C>T synonymous_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 762236 c.2430G>T synonymous_variant 0.12
rpoB 762245 c.2439G>T synonymous_variant 0.11
rpoB 762254 c.2448T>C synonymous_variant 0.12
rpoB 762257 c.2451C>G synonymous_variant 0.12
rpoC 762899 c.-471G>T upstream_gene_variant 0.23
rpoC 762920 c.-450C>T upstream_gene_variant 0.26
rpoC 762929 c.-441G>C upstream_gene_variant 0.25
rpoC 762959 c.-411G>T upstream_gene_variant 0.24
rpoC 762971 c.-399G>C upstream_gene_variant 0.2
rpoC 762983 c.-387C>T upstream_gene_variant 0.16
rpoC 762989 c.-381G>A upstream_gene_variant 0.15
rpoC 762995 c.-375G>T upstream_gene_variant 0.13
rpoB 763002 c.3197dupA frameshift_variant 0.12
rpoB 763006 c.3201delC frameshift_variant 0.13
rpoB 763017 p.Gln1071Glu missense_variant 0.13
rpoC 763528 c.159G>A synonymous_variant 0.25
rpoC 763534 c.165T>C synonymous_variant 0.25
rpoC 763537 c.168C>G synonymous_variant 0.26
rpoC 763546 c.177A>G synonymous_variant 0.3
rpoC 763570 c.201G>C synonymous_variant 0.3
rpoC 763573 c.204G>C synonymous_variant 0.3
rpoC 763594 c.225C>T synonymous_variant 0.27
rpoC 763622 p.Ala85Ser missense_variant 0.15
rpoC 763627 p.Lys86Asn missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471926 n.81C>T non_coding_transcript_exon_variant 0.17
rrs 1471929 n.84C>G non_coding_transcript_exon_variant 0.17
rrs 1471930 n.85G>T non_coding_transcript_exon_variant 0.17
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.18
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.18
rrs 1471936 n.91A>G non_coding_transcript_exon_variant 0.19
rrs 1472085 n.240C>T non_coding_transcript_exon_variant 0.23
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.43
rrs 1472107 n.262A>G non_coding_transcript_exon_variant 0.44
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.44
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.43
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.56
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.56
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.56
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.72
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.71
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.78
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.73
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.79
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.56
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.33
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.83
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.86
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.85
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.85
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.85
rrs 1472427 n.582T>G non_coding_transcript_exon_variant 0.5
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.62
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.82
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.93
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.9
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.89
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.89
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.89
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.89
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.89
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.91
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.9
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.89
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.89
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.89
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.89
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.89
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.92
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.92
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.85
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.73
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.86
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.87
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.88
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.87
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.88
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.9
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.75
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.23
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.33
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.38
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.46
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.8
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.66
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.58
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.47
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.46
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.46
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.46
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.46
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.41
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.38
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.38
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.38
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 1.0
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 1.0
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 1.0
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 1.0
rrl 1474269 n.612C>A non_coding_transcript_exon_variant 1.0
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 1.0
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 1.0
rrl 1474287 n.631_649delCCTTTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.75
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.6
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.67
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.8
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.8
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.8
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.88
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.88
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.88
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.9
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.9
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 1.0
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 1.0
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 1.0
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.55
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.57
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.57
rrl 1474928 n.1271C>T non_coding_transcript_exon_variant 0.33
rrl 1475115 n.1458A>G non_coding_transcript_exon_variant 0.5
rrl 1475124 n.1467A>T non_coding_transcript_exon_variant 0.33
rrl 1475137 n.1480A>T non_coding_transcript_exon_variant 0.57
rrl 1475170 n.1513A>G non_coding_transcript_exon_variant 0.67
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.33
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.2
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.17
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.27
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.27
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.27
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.36
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.42
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.45
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.62
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.6
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.6
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.6
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.67
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.57
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.6
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.6
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.4
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.88
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.91
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.91
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.91
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.91
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.92
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.95
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.79
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.45
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.35
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.26
rpsA 1834024 c.483G>C synonymous_variant 0.12
rpsA 1834034 p.Ile165Val missense_variant 0.11
rpsA 1834039 c.498C>T synonymous_variant 0.12
rpsA 1834040 p.Lys167Gln missense_variant 0.12
rpsA 1834069 c.528G>C synonymous_variant 0.17
rpsA 1834090 c.549G>T synonymous_variant 0.15
rpsA 1834099 c.558C>G synonymous_variant 0.13
rpsA 1834105 c.564C>T synonymous_variant 0.14
rpsA 1834108 c.567C>G synonymous_variant 0.12
rpsA 1834114 c.573G>C synonymous_variant 0.12
rpsA 1834189 c.648G>C synonymous_variant 0.1
rpsA 1834210 c.669C>T synonymous_variant 0.11
rpsA 1834213 c.672G>C synonymous_variant 0.11
rpsA 1834219 c.678C>T synonymous_variant 0.11
rpsA 1834222 c.681T>C synonymous_variant 0.11
rpsA 1834225 c.684C>G synonymous_variant 0.1
rpsA 1834249 c.708T>C synonymous_variant 0.1
rpsA 1834261 c.720A>G synonymous_variant 0.12
rpsA 1834264 c.723G>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168945 c.1668T>C synonymous_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2222013 c.1152C>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247243 p.Gly244Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0