TB-Profiler result

Run: ERR2228815
Summary

Run ID: ERR2228815

Sample name:

Date: 31-03-2023 16:21:51

Number of reads: 880344

Percentage reads mapped: 60.49

Strain: lineage4.8

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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
rpoB 761196 p.Leu464Met missense_variant 0.18 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.42 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.33 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 6042 p.Lys268Met missense_variant 0.2
gyrA 7141 c.-161T>G upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8674 p.Ile458Asn missense_variant 0.2
fgd1 490852 p.Ala24Ser missense_variant 0.19
fgd1 491250 c.468G>T synonymous_variant 0.22
fgd1 491356 p.Phe192Ile missense_variant 0.5
mshA 576150 p.Val268Ala missense_variant 0.2
ccsA 619958 p.Val23Ala missense_variant 0.17
ccsA 620056 p.Thr56Ser missense_variant 0.18
rpoB 761150 c.1344A>C synonymous_variant 0.14
rpoB 761159 c.1353G>C synonymous_variant 0.12
rpoB 761165 c.1359G>C synonymous_variant 0.13
rpoB 761186 p.Glu460Asp missense_variant 0.19
rpoB 761195 c.1389G>C synonymous_variant 0.17
rpoB 762218 c.2412T>C synonymous_variant 0.19
rpoB 762233 c.2427G>C synonymous_variant 0.21
rpoB 762236 c.2430G>T synonymous_variant 0.2
rpoB 762254 c.2448T>C synonymous_variant 0.16
rpoB 762257 c.2451C>G synonymous_variant 0.15
rpoB 762878 p.Ile1024Met missense_variant 0.23
rpoB 762879 p.Met1025Leu missense_variant 0.25
rpoC 762899 c.-471G>T upstream_gene_variant 0.24
rpoC 762920 c.-450C>T upstream_gene_variant 0.29
rpoC 762929 c.-441G>C upstream_gene_variant 0.3
rpoC 762959 c.-411G>T upstream_gene_variant 0.39
rpoC 762971 c.-399G>C upstream_gene_variant 0.29
rpoC 762983 c.-387C>T upstream_gene_variant 0.22
rpoC 762989 c.-381G>A upstream_gene_variant 0.18
rpoC 762995 c.-375G>T upstream_gene_variant 0.19
rpoC 763528 c.159G>A synonymous_variant 0.38
rpoC 763534 c.165T>C synonymous_variant 0.43
rpoC 763537 c.168C>G synonymous_variant 0.41
rpoC 763546 c.177A>G synonymous_variant 0.39
rpoC 763570 c.201G>C synonymous_variant 0.53
rpoC 763573 c.204G>C synonymous_variant 0.5
rpoC 763594 c.225C>T synonymous_variant 0.32
rpoC 763622 p.Ala85Ser missense_variant 0.21
rpoC 763627 p.Lys86Asn missense_variant 0.15
rpoC 763648 c.279C>A synonymous_variant 0.14
rpoC 764232 p.Lys288Arg missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 0.92
mmpL5 776244 p.Ile746Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800758 c.-51A>C upstream_gene_variant 0.18
rplC 800963 p.Leu52Pro missense_variant 0.21
fbiC 1303622 p.Tyr231Cys missense_variant 0.11
fbiC 1303666 p.Thr246Pro missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406211 p.His377Arg missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472085 n.240C>T non_coding_transcript_exon_variant 0.29
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.42
rrs 1472107 n.262A>G non_coding_transcript_exon_variant 0.46
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.38
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.5
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.44
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.5
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.44
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.48
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.61
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.48
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.36
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.32
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.31
rrs 1472286 n.441C>T non_coding_transcript_exon_variant 0.22
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.33
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.38
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.36
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.27
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.33
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.48
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.5
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.59
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.52
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.47
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.48
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.48
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.5
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.6
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.66
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.67
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.65
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.69
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.54
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.68
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.68
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.77
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.71
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.56
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.52
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.68
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.62
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.79
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.71
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.73
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.79
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.53
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.36
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.36
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.44
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.39
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.54
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.29
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.34
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.31
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.32
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.33
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.36
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.38
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.33
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.32
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.32
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.32
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474123 n.466A>G non_coding_transcript_exon_variant 0.2
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.25
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.24
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.26
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.24
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.25
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.19
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.19
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.25
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.13
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.25
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.21
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.21
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.24
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.25
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.29
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.43
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.23
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.24
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.27
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.31
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.29
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.25
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.25
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.24
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.24
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.39
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.33
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.32
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.35
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.33
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.46
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.46
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.39
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.38
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.4
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.55
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.72
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.6
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.5
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.5
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.5
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.44
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.4
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.44
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.35
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.35
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.47
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.41
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.43
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.4
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.38
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.43
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.44
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.56
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.29
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.38
rrl 1476117 n.2460G>A non_coding_transcript_exon_variant 0.44
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.64
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.64
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.67
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.69
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 0.75
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.56
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.69
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.75
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.77
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.75
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.69
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.67
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.75
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.73
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.73
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.57
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.58
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.61
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.61
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.61
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.64
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.64
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.68
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.56
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.59
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.59
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.52
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.3
rpsA 1833909 p.Asp123Gly missense_variant 0.14
tlyA 1917793 c.-147A>C upstream_gene_variant 0.36
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102194 p.Ser283Arg missense_variant 0.2
ndh 2102360 p.Leu228Pro missense_variant 0.13
ndh 2102948 p.Lys32Met missense_variant 0.6
PPE35 2167882 p.Asn911Tyr missense_variant 0.22
PPE35 2168004 p.His870Leu missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169674 p.Asn313Lys missense_variant 0.25
Rv1979c 2222974 p.Val64Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726303 c.111T>A synonymous_variant 0.38
folC 2747640 c.-42G>T upstream_gene_variant 0.22
Rv2752c 3065812 p.Glu127Gly missense_variant 0.12
thyA 3074027 p.Phe149Val missense_variant 0.17
ald 3087654 p.Arg279* stop_gained 0.18
alr 3840482 c.939T>G synonymous_variant 0.17
rpoA 3878490 c.18C>G synonymous_variant 0.38
clpC1 4039121 c.1584T>G synonymous_variant 0.27
embC 4242458 p.Ser866Ala missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244811 p.Cys527Ser missense_variant 0.29
embB 4248813 p.Leu767Pro missense_variant 0.18
aftB 4267774 p.Ile355Phe missense_variant 0.19
ethA 4327524 c.-51A>T upstream_gene_variant 0.43
ethR 4327616 p.Asp23Ala missense_variant 0.17
ethA 4328459 c.-986A>C upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0