TB-Profiler result

Run: ERR037504
Summary

Run ID: ERR037504

Sample name:

Date: 31-03-2023 08:34:14

Number of reads: 8338942

Percentage reads mapped: 64.94

Strain: lineage4.9.1

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
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
lineage4.9.1 Euro-American (H37Rv-like) T1 None 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.45 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.55 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.4 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 8978 c.1677C>T synonymous_variant 1.0
rpoB 761102 c.1296A>G synonymous_variant 0.12
rpoB 761126 c.1320G>C synonymous_variant 0.14
rpoB 761132 c.1326G>C synonymous_variant 0.13
rpoB 761133 c.1327T>C synonymous_variant 0.13
rpoB 761579 c.1773G>C synonymous_variant 0.1
rpoB 762249 p.Leu815Val missense_variant 0.24
rpoC 762836 c.-534C>G upstream_gene_variant 0.28
rpoB 762849 p.Tyr1015Asp missense_variant 0.14
rpoB 762855 p.Val1017Ile missense_variant 0.12
rpoB 762858 p.Thr1018Ser missense_variant 0.14
rpoC 762863 c.-507T>C upstream_gene_variant 0.14
rpoB 762879 p.Met1025Leu missense_variant 0.17
rpoC 762887 c.-483G>C upstream_gene_variant 0.18
rpoC 762929 c.-441G>C upstream_gene_variant 0.22
rpoC 762938 c.-432G>C upstream_gene_variant 0.19
rpoC 762947 c.-423C>G upstream_gene_variant 0.16
rpoC 763492 c.123G>C synonymous_variant 0.12
rpoC 763507 c.138G>C synonymous_variant 0.15
rpoC 763528 c.159G>C synonymous_variant 0.15
rpoC 763532 p.Thr55Ser missense_variant 0.15
rpoC 763570 c.201G>T synonymous_variant 0.17
rpoC 763594 c.225C>T synonymous_variant 0.18
rpoC 763603 c.234C>T synonymous_variant 0.16
rpoC 763609 c.240C>T synonymous_variant 0.12
rpoC 763615 c.246G>C synonymous_variant 0.1
rpoC 763630 c.261G>C synonymous_variant 0.12
rpoC 763633 c.264T>C synonymous_variant 0.11
rpoC 763642 c.273G>C synonymous_variant 0.1
rpoC 764359 c.990C>G synonymous_variant 0.11
rpoC 764605 c.1236G>T synonymous_variant 0.15
rpoC 764611 c.1242G>C synonymous_variant 0.13
rpoC 764620 c.1251G>C synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.13
rpoC 764644 c.1275G>C synonymous_variant 0.15
rpoC 764650 c.1281G>T synonymous_variant 0.17
rpoC 764662 c.1293G>C synonymous_variant 0.14
rpoC 764677 c.1308C>G synonymous_variant 0.16
rpoC 764692 c.1323C>T synonymous_variant 0.15
rpoC 764695 c.1326T>C synonymous_variant 0.15
rpoC 764706 p.Leu446Gln missense_variant 0.16
rpoC 764722 c.1353G>C synonymous_variant 0.18
rpoC 764746 c.1377G>C synonymous_variant 0.25
rpoC 764752 c.1383G>T synonymous_variant 0.23
rpoC 764764 c.1395T>C synonymous_variant 0.23
rpoC 764767 c.1398G>A synonymous_variant 0.19
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471967 n.122G>A non_coding_transcript_exon_variant 0.27
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.27
rrs 1471972 n.127T>C non_coding_transcript_exon_variant 0.27
rrs 1471980 n.135G>T non_coding_transcript_exon_variant 0.28
rrs 1471981 n.136C>G non_coding_transcript_exon_variant 0.28
rrs 1471985 n.140T>C non_coding_transcript_exon_variant 0.27
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.27
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.35
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.37
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.37
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.41
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.57
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.55
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.48
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.31
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.38
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.55
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.55
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.56
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.5
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.32
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.29
rrs 1472495 n.650C>A non_coding_transcript_exon_variant 0.29
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.33
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.56
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.63
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.69
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.69
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.68
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.34
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.28
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.13
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.4
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.51
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.13
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.24
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.55
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.53
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.53
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.54
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.59
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.54
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.53
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.53
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.61
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.61
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.52
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.51
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.53
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.49
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.39
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.36
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.37
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.37
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.37
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.37
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.4
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.41
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.52
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.6
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.53
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.51
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.48
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.28
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.42
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.41
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.29
rrl 1473871 n.214T>C non_coding_transcript_exon_variant 0.42
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.43
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.44
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.38
rrl 1473899 n.242A>T non_coding_transcript_exon_variant 0.36
rrl 1473922 n.265A>T non_coding_transcript_exon_variant 0.17
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.23
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.24
rrl 1474185 n.528G>A non_coding_transcript_exon_variant 0.25
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.4
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.42
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.48
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.41
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.27
rrl 1474281 n.624A>G non_coding_transcript_exon_variant 0.18
rrl 1474316 n.659T>C non_coding_transcript_exon_variant 0.16
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.32
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.31
rrl 1474353 n.696A>T non_coding_transcript_exon_variant 0.32
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.32
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.33
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.34
rrl 1474381 n.724T>C non_coding_transcript_exon_variant 0.3
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.24
rrl 1474450 n.793T>A non_coding_transcript_exon_variant 0.2
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.23
rrl 1474466 n.809G>A non_coding_transcript_exon_variant 0.31
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.35
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.37
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.37
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.39
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.39
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.42
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.37
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.37
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.35
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.36
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.37
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.53
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.46
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.45
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.46
rrl 1474638 n.981C>A non_coding_transcript_exon_variant 0.46
rrl 1474639 n.982G>T non_coding_transcript_exon_variant 0.47
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.4
rrl 1474664 n.1007G>A non_coding_transcript_exon_variant 0.38
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.38
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.2
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.19
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.19
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.2
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.37
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.55
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.53
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.52
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.52
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.62
rrl 1474869 n.1212G>A non_coding_transcript_exon_variant 0.62
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.56
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.56
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.57
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.48
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18
rrl 1475515 n.1858G>A non_coding_transcript_exon_variant 0.35
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.41
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.42
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 0.41
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.41
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.41
rrl 1475548 n.1891C>T non_coding_transcript_exon_variant 0.4
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.12
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.4
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.19
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.2
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.63
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.59
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.58
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.59
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.65
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.59
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.58
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.55
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.46
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.38
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.34
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.31
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.31
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.33
rrl 1475996 n.2339T>A non_coding_transcript_exon_variant 0.13
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.13
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.12
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.17
rrl 1476024 n.2367T>G non_coding_transcript_exon_variant 0.22
rrl 1476025 n.2368G>T non_coding_transcript_exon_variant 0.21
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.2
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.2
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.19
rrl 1476045 n.2388G>C non_coding_transcript_exon_variant 0.19
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.19
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.17
rrl 1476058 n.2401T>C 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 0.28
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.58
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.53
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.48
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.48
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.53
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.52
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.45
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.41
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.4
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.41
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.42
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.42
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.42
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.33
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.44
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.57
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.7
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.64
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.3
rpsA 1833823 c.282G>A synonymous_variant 0.14
rpsA 1833832 c.291G>A synonymous_variant 0.14
rpsA 1833838 c.297G>C synonymous_variant 0.14
rpsA 1833841 c.300C>G synonymous_variant 0.14
rpsA 1833856 c.315A>G synonymous_variant 0.14
rpsA 1833859 c.318C>T synonymous_variant 0.11
rpsA 1833862 c.321G>T synonymous_variant 0.11
rpsA 1834069 c.528G>C synonymous_variant 0.14
rpsA 1834093 c.552G>C synonymous_variant 0.12
rpsA 1834102 c.561T>C synonymous_variant 0.1
rpsA 1834105 c.564C>T synonymous_variant 0.11
rpsA 1834298 p.Gln253Glu missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.15
PPE35 2169866 c.747G>C synonymous_variant 0.3
Rv1979c 2223145 p.Arg7Lys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.27
eis 2715586 c.-254G>C upstream_gene_variant 0.36
pepQ 2859381 c.1038C>G synonymous_variant 0.17
Rv2752c 3064552 p.Arg547Pro missense_variant 0.26
Rv2752c 3067191 c.-1000G>A upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.18
fbiD 3339385 p.Asp90Asn missense_variant 1.0
fbiB 3642734 c.1200G>C synonymous_variant 0.28
rpoA 3878238 p.Asp90Glu missense_variant 0.2
clpC1 4038857 c.1848C>A synonymous_variant 0.19
clpC1 4039691 c.1014G>C synonymous_variant 0.12
clpC1 4039714 p.Tyr331His missense_variant 0.14
clpC1 4039724 c.981A>G synonymous_variant 0.13
clpC1 4039727 c.978C>T synonymous_variant 0.14
clpC1 4039730 c.975C>G synonymous_variant 0.14
clpC1 4039748 c.957G>C synonymous_variant 0.12
clpC1 4039751 c.954A>G synonymous_variant 0.11
clpC1 4039904 c.801A>G synonymous_variant 0.11
clpC1 4039907 c.798G>A synonymous_variant 0.13
clpC1 4039929 c.775_776delAGinsTC synonymous_variant 0.13
clpC1 4039931 p.Gly258Val missense_variant 0.14
clpC1 4039934 c.771G>A synonymous_variant 0.16
clpC1 4039943 c.762G>C synonymous_variant 0.14
clpC1 4039946 c.759A>C synonymous_variant 0.13
clpC1 4039949 c.756G>C synonymous_variant 0.13
clpC1 4039952 c.753T>C synonymous_variant 0.12
clpC1 4040066 c.639G>C synonymous_variant 0.11
clpC1 4040087 c.618G>C synonymous_variant 0.11
clpC1 4040282 c.423G>C synonymous_variant 0.1
clpC1 4040303 c.402G>C synonymous_variant 0.12
clpC1 4040310 p.Thr132Asn missense_variant 0.12
clpC1 4040312 c.393G>C synonymous_variant 0.11
clpC1 4040315 p.Glu130Asp missense_variant 0.11
clpC1 4040324 c.381G>C synonymous_variant 0.11
embC 4239842 c.-21C>A upstream_gene_variant 0.15
embC 4242425 p.Arg855Gly missense_variant 0.17
embC 4242476 p.Pro872Ala missense_variant 0.23
embC 4242822 p.Val987Gly missense_variant 0.39
embC 4242827 p.Leu989Val missense_variant 0.22
ubiA 4269529 p.Ala102Gly missense_variant 0.22
ethA 4327672 c.-199G>A upstream_gene_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0