TB-Profiler result

Run: ERR2432997
Summary

Run ID: ERR2432997

Sample name:

Date: 31-03-2023 18:11:42

Number of reads: 700233

Percentage reads mapped: 76.66

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 1472359 n.514A>C non_coding_transcript_exon_variant 0.83 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.19 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.12 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
rpoB 761051 c.1245G>C synonymous_variant 0.1
rpoB 761054 c.1248G>C synonymous_variant 0.11
rpoB 761060 c.1254C>G synonymous_variant 0.11
rpoB 761066 c.1260G>C synonymous_variant 0.1
rpoB 761084 c.1278C>G synonymous_variant 0.11
rpoB 761087 c.1281C>G synonymous_variant 0.11
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.12
rpoB 761102 c.1296A>G synonymous_variant 0.13
rpoB 761105 c.1299C>T synonymous_variant 0.88
rpoB 762122 p.Asp772Glu missense_variant 0.12
rpoB 762128 c.2322G>C synonymous_variant 0.13
rpoB 762131 c.2325C>G synonymous_variant 0.12
rpoB 762134 c.2328C>G synonymous_variant 0.12
rpoB 762140 c.2334G>C synonymous_variant 0.12
rpoB 762143 c.2337T>C synonymous_variant 0.12
rpoB 762149 c.2343G>C synonymous_variant 0.12
rpoB 762156 p.Val784Ile missense_variant 0.11
rpoB 762167 c.2361T>C synonymous_variant 0.11
rpoB 762174 c.2370delT frameshift_variant 0.11
rpoB 762181 p.Asp792Gly missense_variant 0.11
rpoC 762899 c.-471G>C upstream_gene_variant 0.14
rpoC 762917 c.-453C>G upstream_gene_variant 0.17
rpoC 762923 c.-447C>G upstream_gene_variant 0.17
rpoC 762929 c.-441G>C upstream_gene_variant 0.17
rpoC 762947 c.-423C>G upstream_gene_variant 0.24
rpoC 762962 c.-408C>T upstream_gene_variant 0.24
rpoC 762995 c.-375G>C upstream_gene_variant 0.22
rpoB 763005 p.Cys1067Val missense_variant 0.24
rpoB 763014 p.Met1070Leu missense_variant 0.23
rpoB 763017 p.Gln1071Glu missense_variant 0.23
rpoC 763022 c.-348C>G upstream_gene_variant 0.21
rpoC 763028 c.-342T>C upstream_gene_variant 0.22
rpoC 763040 c.-330C>G upstream_gene_variant 0.21
rpoC 763052 c.-318G>C upstream_gene_variant 0.18
rpoC 763053 c.-317_-315delTTGinsCTC upstream_gene_variant 0.18
rpoC 763070 c.-300T>C upstream_gene_variant 0.16
rpoB 763072 c.3268_3270delACC conservative_inframe_deletion 0.16
rpoB 763078 c.3272_3273insGCC disruptive_inframe_insertion 0.17
rpoC 763537 c.168C>G synonymous_variant 0.12
rpoC 763546 c.177A>G synonymous_variant 0.13
rpoC 763570 c.201G>C synonymous_variant 0.18
rpoC 763615 c.246G>C synonymous_variant 0.19
rpoC 763618 c.249C>G synonymous_variant 0.19
rpoC 763622 p.Ala85Ser missense_variant 0.19
rpoC 763630 c.261G>C synonymous_variant 0.19
rpoC 763633 c.264T>C synonymous_variant 0.19
rpoC 763642 c.273G>C synonymous_variant 0.19
rpoC 763660 c.291T>C synonymous_variant 0.19
rpoC 763675 c.306C>G synonymous_variant 0.19
rpoC 763686 p.Tyr106Phe missense_variant 0.19
rpoC 763702 c.333C>G synonymous_variant 0.17
rpoC 763708 c.339G>C synonymous_variant 0.18
rpoC 763711 c.342G>C synonymous_variant 0.15
rpoC 763714 c.345G>C synonymous_variant 0.15
rpoC 763717 c.348T>C synonymous_variant 0.15
rpoC 763723 c.354G>C synonymous_variant 0.14
rpoC 764507 p.Ala380Ser missense_variant 0.11
rpoC 764521 c.1152T>C synonymous_variant 0.11
rpoC 764611 c.1242G>C synonymous_variant 0.14
rpoC 764632 c.1263T>C synonymous_variant 0.12
rpoC 764650 c.1281G>T synonymous_variant 0.16
rpoC 764662 c.1293G>C synonymous_variant 0.18
rpoC 764706 p.Leu446Gln missense_variant 0.2
rpoC 764716 c.1347G>C synonymous_variant 0.19
rpoC 764722 c.1353G>C synonymous_variant 0.16
rpoC 764746 c.1377G>C synonymous_variant 0.17
rpoC 764749 c.1380G>C synonymous_variant 0.17
rpoC 764764 c.1395T>C synonymous_variant 0.17
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.17
rpoC 764785 c.1416C>G synonymous_variant 0.18
rpoC 764797 c.1428G>C synonymous_variant 0.17
rpoC 764804 p.Gln479Ala missense_variant 0.14
rpoC 764812 c.1443C>G synonymous_variant 0.14
rpoC 764813 p.Gln482Val missense_variant 0.13
rpoC 764824 c.1455T>C synonymous_variant 0.13
rpoC 764833 c.1464A>G synonymous_variant 0.15
rpoC 764843 p.Ala492Thr missense_variant 0.16
rpoC 764857 c.1488G>C synonymous_variant 0.11
rpoC 764858 c.1489T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406302 c.1039C>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.14
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.15
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.18
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.23
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.19
rrs 1472434 n.589_590insC non_coding_transcript_exon_variant 0.13
rrs 1472437 n.592T>C non_coding_transcript_exon_variant 0.14
rrs 1472438 n.594delC non_coding_transcript_exon_variant 0.14
rrs 1472446 n.602dupC non_coding_transcript_exon_variant 0.14
rrs 1472450 n.606delC non_coding_transcript_exon_variant 0.14
rrs 1472456 n.611T>C non_coding_transcript_exon_variant 0.15
rrs 1472460 n.615T>C non_coding_transcript_exon_variant 0.15
rrs 1472461 n.616G>T non_coding_transcript_exon_variant 0.15
rrs 1472462 n.617T>G non_coding_transcript_exon_variant 0.15
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.15
rrs 1472467 n.622G>T non_coding_transcript_exon_variant 0.15
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.15
rrs 1472473 n.628G>T non_coding_transcript_exon_variant 0.15
rrs 1472474 n.629C>G non_coding_transcript_exon_variant 0.15
rrs 1472476 n.631A>G non_coding_transcript_exon_variant 0.15
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.15
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.16
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.16
rrs 1472504 n.659A>T non_coding_transcript_exon_variant 0.17
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.11
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.11
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.12
rrs 1472583 n.738T>C non_coding_transcript_exon_variant 0.12
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.11
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.1
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.1
rrs 1472863 n.1018T>C non_coding_transcript_exon_variant 0.1
rrs 1472867 n.1022T>G non_coding_transcript_exon_variant 0.11
rrs 1472869 n.1024G>A non_coding_transcript_exon_variant 0.1
rrs 1472870 n.1025T>A non_coding_transcript_exon_variant 0.11
rrs 1472873 n.1028C>T non_coding_transcript_exon_variant 0.12
rrs 1472875 n.1030T>G non_coding_transcript_exon_variant 0.12
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.14
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.21
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.21
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.16
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.16
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.16
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.16
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.17
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.13
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.13
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.18
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.18
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.18
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.17
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.17
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.21
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.26
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.19
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.19
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.15
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.16
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.12
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.12
rrl 1474630 n.973T>C non_coding_transcript_exon_variant 0.12
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.12
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.12
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.12
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.12
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.22
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.23
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.23
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.33
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.33
rrl 1474717 n.1060_1061insGCCAG non_coding_transcript_exon_variant 0.33
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.32
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.31
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.3
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.3
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.29
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.29
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.26
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.24
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.23
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.23
rrl 1475186 n.1529C>A non_coding_transcript_exon_variant 0.15
rrl 1476146 n.2489G>T non_coding_transcript_exon_variant 0.15
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.14
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.21
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.15
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.15
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.25
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.27
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.27
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.27
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.27
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.27
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.22
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.18
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.17
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.17
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.17
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.16
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.16
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.15
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.53
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.47
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.4
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.38
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.38
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.38
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.38
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.38
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.38
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.24
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.24
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.21
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.21
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.19
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.18
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.18
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.18
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.2
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.2
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.2
rrl 1476661 n.3004A>G non_coding_transcript_exon_variant 0.19
rrl 1476665 n.3008T>G non_coding_transcript_exon_variant 0.2
rrl 1476668 n.3011C>T non_coding_transcript_exon_variant 0.2
rrl 1476675 n.3018C>G non_coding_transcript_exon_variant 0.17
rrl 1476682 n.3026delT non_coding_transcript_exon_variant 0.18
inhA 1674542 p.Ala114Val missense_variant 0.13
inhA 1674672 c.471C>A synonymous_variant 0.11
rpsA 1833874 c.333T>C synonymous_variant 0.19
rpsA 1833877 c.336C>G synonymous_variant 0.19
rpsA 1833886 c.345C>G synonymous_variant 0.15
rpsA 1833893 p.Ala118Lys missense_variant 0.18
rpsA 1833896 p.Leu119Ile missense_variant 0.19
rpsA 1833905 p.Lys122Glu missense_variant 0.2
rpsA 1833912 p.Glu124Gly missense_variant 0.21
rpsA 1833915 p.Ala125Val missense_variant 0.21
rpsA 1833921 p.Lys127Thr missense_variant 0.25
rpsA 1833928 c.387G>C synonymous_variant 0.23
rpsA 1833949 c.408T>C synonymous_variant 0.23
rpsA 1833955 c.414G>C synonymous_variant 0.2
rpsA 1833970 c.429G>T synonymous_variant 0.22
rpsA 1833979 c.438T>C synonymous_variant 0.2
rpsA 1833997 c.456G>C synonymous_variant 0.19
rpsA 1834000 c.459G>C synonymous_variant 0.19
rpsA 1834009 c.468C>T synonymous_variant 0.2
rpsA 1834012 c.471G>T synonymous_variant 0.2
rpsA 1834024 c.483G>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878595 c.-88C>T upstream_gene_variant 0.67
clpC1 4039691 c.1014G>C synonymous_variant 0.14
clpC1 4039711 p.Ile332Val missense_variant 0.12
clpC1 4039724 c.981A>G synonymous_variant 0.13
clpC1 4039736 c.969C>G synonymous_variant 0.12
clpC1 4039739 c.966C>G synonymous_variant 0.12
clpC1 4039751 c.954A>G synonymous_variant 0.12
clpC1 4039757 c.948A>G synonymous_variant 0.17
clpC1 4039766 c.939T>C synonymous_variant 0.12
clpC1 4039769 c.936C>G synonymous_variant 0.12
clpC1 4039773 p.Lys311Met missense_variant 0.12
clpC1 4039778 c.927A>G synonymous_variant 0.12
clpC1 4039781 c.924G>C synonymous_variant 0.12
clpC1 4039787 c.916_918delTCGinsAGC synonymous_variant 0.13
clpC1 4039817 c.888A>T synonymous_variant 0.2
clpC1 4039820 c.885T>G synonymous_variant 0.21
clpC1 4039829 c.874_876delTTGinsCTC synonymous_variant 0.22
clpC1 4039832 c.873C>G synonymous_variant 0.22
clpC1 4039838 p.Leu289Ile missense_variant 0.23
clpC1 4039850 c.855T>C synonymous_variant 0.21
clpC1 4039865 c.840T>C synonymous_variant 0.24
clpC1 4039871 c.834C>G synonymous_variant 0.23
clpC1 4039875 p.Asn277Arg missense_variant 0.24
clpC1 4039898 c.807C>G synonymous_variant 0.3
clpC1 4039904 c.801A>G synonymous_variant 0.3
clpC1 4039925 c.780C>G synonymous_variant 0.27
clpC1 4039931 c.774T>C synonymous_variant 0.25
clpC1 4039937 c.768G>C synonymous_variant 0.23
clpC1 4039945 p.Ser254Ala missense_variant 0.24
clpC1 4039946 c.759A>C synonymous_variant 0.24
clpC1 4039949 c.756G>C synonymous_variant 0.24
clpC1 4039952 c.753T>C synonymous_variant 0.24
clpC1 4039955 c.750G>C synonymous_variant 0.24
clpC1 4039979 c.726C>G synonymous_variant 0.27
clpC1 4039988 c.717C>G synonymous_variant 0.28
clpC1 4039994 p.Glu237Asp missense_variant 0.28
clpC1 4040001 p.His235Arg missense_variant 0.24
clpC1 4040010 p.Ala232Asp missense_variant 0.28
clpC1 4040018 c.687G>C synonymous_variant 0.25
clpC1 4040021 c.684A>C synonymous_variant 0.24
clpC1 4040024 c.681A>G synonymous_variant 0.27
clpC1 4040033 c.672G>C synonymous_variant 0.17
clpC1 4040036 c.669C>G synonymous_variant 0.21
clpC1 4040063 c.642G>C synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0