TB-Profiler result

Run: ERR4596904
Summary

Run ID: ERR4596904

Sample name:

Date: 01-04-2023 06:28:52

Number of reads: 3983082

Percentage reads mapped: 71.18

Strain: lineage3.1.1

Drug-resistance: MDR-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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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 761116 p.Asn437Thr missense_variant 0.13 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.9 rifampicin
katG 2155142 p.Thr324Pro missense_variant 1.0 isoniazid
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.19
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761015 c.1209G>C synonymous_variant 0.12
rpoB 761027 c.1221A>G synonymous_variant 0.12
rpoB 761036 c.1230G>C synonymous_variant 0.11
rpoB 761066 c.1260G>C synonymous_variant 0.11
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.13
rpoB 761102 c.1296A>G synonymous_variant 0.14
rpoB 761133 c.1327T>C synonymous_variant 0.13
rpoB 761147 c.1341C>T synonymous_variant 0.12
rpoB 761150 c.1344A>T synonymous_variant 0.12
rpoB 762128 c.2322G>C synonymous_variant 0.1
rpoB 762161 c.2355C>G synonymous_variant 0.11
rpoB 762194 c.2388G>C synonymous_variant 0.1
rpoB 762233 c.2427G>C synonymous_variant 0.12
rpoB 762236 c.2430G>C synonymous_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763486 c.117T>C synonymous_variant 0.12
rpoC 763492 c.123G>C synonymous_variant 0.12
rpoC 763495 c.126G>A synonymous_variant 0.12
rpoC 763504 c.135C>A synonymous_variant 0.14
rpoC 763507 c.138G>C synonymous_variant 0.14
rpoC 763528 c.159G>T synonymous_variant 0.14
rpoC 763534 c.165T>C synonymous_variant 0.15
rpoC 763537 c.168C>G synonymous_variant 0.16
rpoC 763546 c.177A>G synonymous_variant 0.17
rpoC 763558 c.189C>T synonymous_variant 0.2
rpoC 763570 c.201G>C synonymous_variant 0.19
rpoC 763573 c.204G>C synonymous_variant 0.2
rpoC 763615 c.246G>T synonymous_variant 0.18
rpoC 763618 c.249C>T synonymous_variant 0.16
rpoC 763633 c.264T>G synonymous_variant 0.14
rpoC 763660 c.291T>G synonymous_variant 0.16
rpoC 763666 c.297G>T synonymous_variant 0.16
rpoC 763704 p.Ser112Trp missense_variant 0.11
rpoC 763717 c.348T>C synonymous_variant 0.1
rpoC 764428 c.1059G>C synonymous_variant 0.11
rpoC 764458 c.1089G>C synonymous_variant 0.11
rpoC 764470 c.1101C>G synonymous_variant 0.11
rpoC 764497 c.1128A>G synonymous_variant 0.12
rpoC 764498 p.Ser377Ala missense_variant 0.12
rpoC 764503 c.1134G>C synonymous_variant 0.11
rpoC 764626 c.1257C>T synonymous_variant 0.13
rpoC 764646 p.Gly426Ala missense_variant 0.14
rpoC 764650 c.1281G>T synonymous_variant 0.12
rpoC 764653 c.1284G>C synonymous_variant 0.12
rpoC 764662 c.1293G>C synonymous_variant 0.13
rpoC 764705 p.Leu446Ala missense_variant 0.13
rpoC 764722 c.1353G>C synonymous_variant 0.19
rpoC 764746 c.1377G>C synonymous_variant 0.19
rpoC 764764 c.1395T>C synonymous_variant 0.17
rpoC 764785 c.1416C>G synonymous_variant 0.12
rpoC 764797 c.1428G>C synonymous_variant 0.11
rpoC 764809 c.1440C>G synonymous_variant 0.11
rpoC 764812 c.1443C>G synonymous_variant 0.11
rpoC 764815 p.Gln482His missense_variant 0.1
rpoC 764824 c.1455T>C synonymous_variant 0.1
rpoC 764858 c.1489T>C synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.35
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.48
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.49
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.46
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.41
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.37
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.17
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.15
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.15
rrs 1472293 n.448C>A non_coding_transcript_exon_variant 0.15
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 0.17
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.17
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.16
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.16
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.16
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.17
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.19
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.2
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.2
rrs 1472486 n.641A>G non_coding_transcript_exon_variant 0.17
rrs 1472494 n.649A>T non_coding_transcript_exon_variant 0.17
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.19
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.19
rrs 1472507 n.662C>T non_coding_transcript_exon_variant 0.22
rrs 1472508 n.663T>C non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.37
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.37
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.37
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.38
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.44
rrs 1472660 n.815T>A non_coding_transcript_exon_variant 0.42
rrs 1472673 n.828T>C non_coding_transcript_exon_variant 0.36
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.36
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.37
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.37
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.37
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.37
rrs 1472685 n.840G>T non_coding_transcript_exon_variant 0.37
rrs 1472686 n.841G>C non_coding_transcript_exon_variant 0.37
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.37
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.38
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.38
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.17
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.24
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.24
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.25
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.24
rrs 1472969 n.1124_1125insTGCCCTT non_coding_transcript_exon_variant 0.25
rrs 1472972 n.1127T>G non_coding_transcript_exon_variant 0.24
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.25
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.25
rrs 1472977 n.1132G>A non_coding_transcript_exon_variant 0.25
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 1472989 n.1144G>A non_coding_transcript_exon_variant 0.27
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.27
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.43
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.46
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.47
rrs 1473062 n.1217T>G non_coding_transcript_exon_variant 0.49
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.5
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.51
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.51
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.55
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.55
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.55
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.54
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.54
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.53
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.57
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.54
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.55
rrs 1473201 n.1356A>T non_coding_transcript_exon_variant 0.5
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.49
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.45
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.41
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.37
rrs 1473299 n.1454G>A non_coding_transcript_exon_variant 0.33
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.34
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.34
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.36
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.36
rrl 1474476 n.819C>G non_coding_transcript_exon_variant 0.11
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.13
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.12
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.13
rrl 1474497 n.840G>A non_coding_transcript_exon_variant 0.12
rrl 1474506 n.849C>T non_coding_transcript_exon_variant 0.13
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.13
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.13
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.13
rrl 1474528 n.871T>A non_coding_transcript_exon_variant 0.13
rrl 1474529 n.872A>G non_coding_transcript_exon_variant 0.14
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.13
rrl 1474540 n.883T>C non_coding_transcript_exon_variant 0.13
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.13
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.13
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.15
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.21
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.17
rrl 1474628 n.971C>T non_coding_transcript_exon_variant 0.16
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.17
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.17
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.17
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.17
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.18
rrl 1474651 n.995delT non_coding_transcript_exon_variant 0.22
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.27
rrl 1474662 n.1005C>G non_coding_transcript_exon_variant 0.28
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.3
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.3
rrl 1474688 n.1031G>C non_coding_transcript_exon_variant 0.34
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.35
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.35
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.33
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.37
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.42
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.44
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.42
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.45
rrl 1474777 n.1120T>G non_coding_transcript_exon_variant 0.43
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.43
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.43
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.44
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.48
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.41
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.38
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.23
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.23
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.23
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.31
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.32
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.33
rrl 1475740 n.2083G>C non_coding_transcript_exon_variant 0.44
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.43
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.43
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.25
rrl 1475761 n.2104C>T non_coding_transcript_exon_variant 0.18
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.18
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.32
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.46
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.48
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.49
rrl 1475883 n.2226A>G non_coding_transcript_exon_variant 0.63
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.6
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.62
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.52
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.6
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.58
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.58
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.58
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 0.43
rrl 1475982 n.2325G>A non_coding_transcript_exon_variant 0.43
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.43
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.43
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.44
rrl 1476025 n.2368G>T non_coding_transcript_exon_variant 0.14
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.12
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 0.2
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.26
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.33
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.34
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.32
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.32
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.31
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.36
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.36
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.39
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.39
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.38
rrl 1476255 n.2598A>G non_coding_transcript_exon_variant 0.37
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.37
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.37
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.37
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.35
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.32
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.29
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.28
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.28
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.28
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.28
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.27
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.28
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.28
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.29
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.47
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.45
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.54
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.47
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.34
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.34
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.34
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.34
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.32
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.31
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.34
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.34
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.32
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.33
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.24
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.23
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.2
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.18
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.11
rpsA 1834264 c.723G>C synonymous_variant 0.12
rpsA 1834285 c.744G>C synonymous_variant 0.11
rpsA 1834294 c.753G>C synonymous_variant 0.12
rpsA 1834298 p.Gln253Glu missense_variant 0.13
rpsA 1834303 c.762T>C synonymous_variant 0.11
rpsA 1834306 c.765T>C synonymous_variant 0.11
rpsA 1834307 p.Asp256His missense_variant 0.11
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 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039982 c.723G>C synonymous_variant 0.12
clpC1 4040000 p.His235Lys missense_variant 0.14
clpC1 4040003 c.702G>C synonymous_variant 0.14
clpC1 4040021 c.684A>C synonymous_variant 0.13
clpC1 4040024 c.681A>G synonymous_variant 0.14
clpC1 4040036 c.669C>G synonymous_variant 0.14
clpC1 4040063 c.642G>C synonymous_variant 0.11
clpC1 4040066 c.639G>C synonymous_variant 0.11
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0