TB-Profiler result

Run: ERR2512849
Summary

Run ID: ERR2512849

Sample name:

Date: 31-03-2023 19:17:48

Number of reads: 1439131

Percentage reads mapped: 75.47

Strain: lineage1.1.3.1

Drug-resistance: RR-TB

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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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.99
lineage1.1.3.1 Indo-Oceanic NA RD239 0.99
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 761127 p.Ser441Ala missense_variant 0.1 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.47 streptomycin
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 5117 c.-123G>A upstream_gene_variant 0.67
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760561 c.757_758delCG frameshift_variant 0.13
rpoB 760567 p.Ser254Trp missense_variant 0.13
rpoB 760571 c.765G>C synonymous_variant 0.12
rpoB 760591 p.Val262Ala missense_variant 0.17
rpoB 760595 c.789C>T synonymous_variant 0.17
rpoB 760596 p.Thr264Pro missense_variant 0.17
rpoB 760611 c.805T>C synonymous_variant 0.16
rpoB 760817 c.1011A>G synonymous_variant 0.2
rpoB 760820 c.1014T>C synonymous_variant 0.22
rpoB 760826 c.1020C>G synonymous_variant 0.2
rpoB 760830 c.1024T>C synonymous_variant 0.2
rpoB 760841 c.1035T>C synonymous_variant 0.18
rpoB 760858 p.Val351Ala missense_variant 0.14
rpoB 760862 c.1056G>C synonymous_variant 0.14
rpoB 760865 c.1059C>T synonymous_variant 0.17
rpoB 760886 p.Glu360Asp missense_variant 0.22
rpoB 760887 p.Thr361Val missense_variant 0.2
rpoB 760910 c.1104C>T synonymous_variant 0.15
rpoB 760916 c.1110C>T synonymous_variant 0.12
rpoB 760928 c.1122G>C synonymous_variant 0.12
rpoB 761030 c.1224G>C synonymous_variant 0.14
rpoB 761037 c.1231T>C synonymous_variant 0.17
rpoB 761051 c.1245G>C synonymous_variant 0.16
rpoB 761054 c.1248G>C synonymous_variant 0.15
rpoB 761057 c.1251G>C synonymous_variant 0.14
rpoB 761060 c.1254C>G synonymous_variant 0.14
rpoB 761084 c.1278C>A synonymous_variant 0.12
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.12
rpoB 761096 c.1290G>C synonymous_variant 0.12
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.12
rpoB 761102 c.1296A>G synonymous_variant 0.11
rpoB 761132 c.1326G>C synonymous_variant 0.11
rpoB 761165 c.1359G>C synonymous_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764497 c.1128A>G synonymous_variant 0.1
rpoC 764510 c.1141C>T synonymous_variant 0.12
rpoC 764521 c.1152T>C synonymous_variant 0.22
rpoC 764527 c.1158C>T synonymous_variant 0.14
rpoC 764530 c.1161C>T synonymous_variant 0.15
rpoC 764533 c.1164C>A synonymous_variant 0.14
rpoC 764536 c.1167G>T synonymous_variant 0.23
rpoC 764539 c.1170C>G synonymous_variant 0.21
rpoC 764548 c.1179G>A synonymous_variant 0.17
rpoC 764573 p.Leu402Ile missense_variant 0.24
rpoC 764578 c.1209C>G synonymous_variant 0.21
rpoC 764581 c.1212T>C synonymous_variant 0.24
rpoC 764582 p.Leu405Met missense_variant 0.25
rpoC 764602 c.1233C>T synonymous_variant 0.17
rpoC 764605 c.1236G>T synonymous_variant 0.17
rpoC 764611 c.1242G>T synonymous_variant 0.22
rpoC 764647 c.1278C>T synonymous_variant 0.14
rpoC 764650 c.1281G>T synonymous_variant 0.14
rpoC 764662 c.1293G>C synonymous_variant 0.12
rpoC 764677 c.1308C>G synonymous_variant 0.11
rpoC 764678 p.Lys437Gln missense_variant 0.11
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766837 c.3468G>C synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776053 c.2428T>C synonymous_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779526 c.-621G>A upstream_gene_variant 1.0
mmpS5 779594 c.-689T>C upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.14
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.16
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.32
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.32
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.32
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.53
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.48
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.35
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.38
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.43
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.23
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.2
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.56
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.56
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.56
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.55
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.55
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.59
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.59
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.61
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.65
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.65
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.78
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.76
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.76
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.21
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.14
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.68
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.55
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.15
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.55
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.53
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 0.53
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.56
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.53
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.59
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.53
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.63
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.61
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.63
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.17
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.57
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.44
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.44
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.11
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.38
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.35
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.44
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.62
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.29
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.57
rrs 1472840 n.995A>G non_coding_transcript_exon_variant 0.33
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.44
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.15
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.31
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.38
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.23
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.44
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.31
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.17
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.27
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.27
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.55
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.21
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.32
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.83
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.69
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.79
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.72
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.17
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.27
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.7
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.72
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.74
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.65
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.76
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.76
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.76
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.42
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.77
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.35
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.22
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.79
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.77
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.43
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.41
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.54
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.8
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.84
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.67
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.62
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.56
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.6
rrl 1473384 n.-274A>G upstream_gene_variant 0.2
rrl 1473428 n.-230A>C upstream_gene_variant 0.22
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.33
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.33
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.25
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.22
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.27
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.18
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.2
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.18
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.4
rrl 1474637 n.980C>G non_coding_transcript_exon_variant 0.4
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.5
rrl 1474643 n.986A>G non_coding_transcript_exon_variant 0.5
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.5
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.5
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.5
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.67
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.67
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 0.67
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.5
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.56
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.44
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.4
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.2
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.18
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.14
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.14
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.25
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.25
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.38
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.25
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.25
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.38
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.33
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.33
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.33
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.33
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.38
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.5
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.5
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.2
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.81
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.35
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.54
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.46
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.31
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.38
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.13
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.14
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.43
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.33
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.31
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.25
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.23
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.17
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.15
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rpsA 1834264 c.723G>C synonymous_variant 0.13
rpsA 1834294 c.753G>C synonymous_variant 0.14
rpsA 1834298 p.Gln253Glu missense_variant 0.14
rpsA 1834306 c.765T>C synonymous_variant 0.17
rpsA 1834307 p.Asp256Gln missense_variant 0.12
rpsA 1834312 c.771G>A synonymous_variant 0.12
rpsA 1834327 c.786G>T synonymous_variant 0.16
rpsA 1834345 c.804C>T synonymous_variant 0.14
rpsA 1834348 c.807T>C synonymous_variant 0.11
rpsA 1834354 c.813G>C synonymous_variant 0.11
rpsA 1834357 c.816T>C synonymous_variant 0.13
rpsA 1834375 c.834G>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168089 p.Pro842Ser missense_variant 0.12
PPE35 2168286 c.2326delA frameshift_variant 0.15
PPE35 2168677 p.Leu646Ile missense_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448331 c.-173G>T upstream_gene_variant 0.11
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449037 p.Lys178Asn missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3841253 c.168C>T synonymous_variant 1.0
clpC1 4038812 c.1893T>C synonymous_variant 0.12
clpC1 4038878 c.1827A>G synonymous_variant 0.12
clpC1 4039409 c.1296T>C synonymous_variant 0.1
clpC1 4039412 c.1293T>G synonymous_variant 0.12
clpC1 4039430 c.1275T>C synonymous_variant 0.13
clpC1 4039442 c.1263A>G synonymous_variant 0.15
clpC1 4039466 c.1239T>C synonymous_variant 0.13
clpC1 4039469 c.1236T>C synonymous_variant 0.14
clpC1 4039472 c.1233G>C synonymous_variant 0.13
clpC1 4039478 c.1227G>C synonymous_variant 0.13
clpC1 4039481 c.1224T>C synonymous_variant 0.13
clpC1 4039487 c.1218G>C synonymous_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.94
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407734 p.Gly157Arg missense_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0