TB-Profiler result

Run: SRR1062895
Summary

Run ID: SRR1062895

Sample name:

Date: 02-04-2023 18:39:06

Number of reads: 434795

Percentage reads mapped: 18.54

Strain: lineage4.6.1.1

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.99
lineage4.6.1.1 Euro-American T2-Uganda RD724 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
ethA 4326796 c.677delA frameshift_variant 0.4 ethionamide
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 5283 p.Ala15Gly missense_variant 0.14
gyrB 5299 c.60C>A synonymous_variant 0.18
gyrB 5953 c.714C>T synonymous_variant 0.29
gyrB 6084 p.Gly282Ala missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491147 p.Trp122Leu missense_variant 0.12
mshA 575763 p.Ala139Asp missense_variant 0.17
rpoB 760343 c.537G>T synonymous_variant 0.17
rpoC 762425 c.-945C>A upstream_gene_variant 0.2
rpoC 762887 c.-483G>C upstream_gene_variant 0.38
rpoC 762899 c.-471G>C upstream_gene_variant 0.41
rpoC 762917 c.-453C>G upstream_gene_variant 0.41
rpoC 762920 c.-450C>T upstream_gene_variant 0.44
rpoC 762923 c.-447C>G upstream_gene_variant 0.44
rpoB 762925 p.Thr1040Ile missense_variant 0.44
rpoB 762934 c.3129_3130insAGCC frameshift_variant 0.41
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.41
rpoC 762989 c.-381G>C upstream_gene_variant 0.22
rpoC 764566 c.1197C>G synonymous_variant 0.25
rpoC 764575 c.1206T>G synonymous_variant 0.25
rpoC 764581 c.1212T>C synonymous_variant 0.28
rpoC 764582 p.Leu405Met missense_variant 0.32
rpoC 764587 c.1218C>G synonymous_variant 0.32
rpoC 764593 c.1224C>T synonymous_variant 0.37
rpoC 764605 c.1236G>C synonymous_variant 0.48
rpoC 764611 c.1242G>T synonymous_variant 0.44
rpoC 764632 c.1263T>C synonymous_variant 0.56
rpoC 764641 c.1272C>T synonymous_variant 0.58
rpoC 764650 c.1281G>T synonymous_variant 0.57
rpoC 764663 p.Val432Thr missense_variant 0.5
rpoC 764672 p.Gln435Glu missense_variant 0.46
rpoC 764677 c.1308C>G synonymous_variant 0.44
rpoC 764695 c.1326T>C synonymous_variant 0.42
rpoC 764701 c.1332C>G synonymous_variant 0.33
rpoC 764705 p.Leu446Lys missense_variant 0.37
rpoC 764716 c.1347G>C synonymous_variant 0.29
rpoC 766778 p.Glu1137* stop_gained 0.2
rpoC 767000 p.Thr1211Ala missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777747 p.Gly245Ala missense_variant 0.15
mmpR5 778277 c.-713C>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303135 p.Gly69Ser missense_variant 0.22
fbiC 1303326 c.396C>A synonymous_variant 0.29
fbiC 1305213 c.2283C>G synonymous_variant 0.15
embR 1416559 p.Lys263Asn missense_variant 0.25
embR 1417229 p.Ala40Asp missense_variant 0.33
atpE 1461009 c.-36G>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.14
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.15
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.15
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.3
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.58
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.74
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.78
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.75
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.79
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.79
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.73
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.71
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.63
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.65
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.65
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.6
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.25
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.42
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.42
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.42
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.38
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.47
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.44
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.44
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.44
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.4
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.33
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.33
rrs 1472425 n.580T>C non_coding_transcript_exon_variant 0.15
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.8
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.75
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.76
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.91
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.93
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.95
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.93
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.91
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.9
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.85
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.82
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.33
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.33
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.33
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.33
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.29
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.29
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.29
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.2
rrs 1473223 n.1378G>A non_coding_transcript_exon_variant 0.22
rrl 1474214 n.557G>C non_coding_transcript_exon_variant 0.2
rrl 1474946 n.1289C>T non_coding_transcript_exon_variant 0.25
rrl 1475245 n.1588T>C non_coding_transcript_exon_variant 0.33
rrl 1475635 n.1978G>A non_coding_transcript_exon_variant 0.15
rrl 1475641 n.1984G>A non_coding_transcript_exon_variant 0.15
rrl 1475790 n.2133C>A non_coding_transcript_exon_variant 0.23
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.3
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.61
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.61
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.61
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.61
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.53
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.53
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.14
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.69
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.78
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.78
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.82
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.83
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.87
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.86
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.89
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.89
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.93
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.92
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.91
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.9
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.88
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.86
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.86
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.86
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.83
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.82
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.6
rrl 1476563 n.2906G>T non_coding_transcript_exon_variant 0.4
fabG1 1673269 c.-171G>T upstream_gene_variant 0.29
fabG1 1673890 p.Ala151Ser missense_variant 0.29
rpsA 1833982 p.Phe147Leu missense_variant 0.25
rpsA 1833990 p.Ala150Asp missense_variant 0.25
rpsA 1834595 p.Asp352Asn missense_variant 0.33
rpsA 1834770 p.Gln410Leu missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101775 p.Ser423Ile missense_variant 0.15
PPE35 2168962 p.Gly551Cys missense_variant 0.15
Rv1979c 2221800 c.1365G>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517924 c.-191G>T upstream_gene_variant 0.29
kasA 2518511 p.Gly133Ser missense_variant 0.15
eis 2714854 p.Gly160Val missense_variant 0.29
eis 2715252 p.Phe27Leu missense_variant 0.33
folC 2747065 c.533delG frameshift_variant 0.29
Rv3083 3448840 p.Gln113* stop_gained 0.17
Rv3083 3449859 c.1356G>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474145 p.Gly47Arg missense_variant 0.15
fprA 3474266 p.His87Arg missense_variant 0.17
fbiB 3640560 c.-975G>A upstream_gene_variant 0.22
fbiA 3641031 p.Ser163Arg missense_variant 0.67
ddn 3986930 p.Tyr29* stop_gained 0.18
ddn 3987002 c.159C>A synonymous_variant 0.12
clpC1 4039590 c.1114delG frameshift_variant 0.15
clpC1 4039600 p.His369Asn missense_variant 0.14
clpC1 4039667 p.Gln346Phe missense_variant 0.12
clpC1 4039682 c.1023C>G synonymous_variant 0.12
clpC1 4039690 p.Glu339Gln missense_variant 0.12
clpC1 4039691 c.1014G>C synonymous_variant 0.12
clpC1 4039697 c.1008C>G synonymous_variant 0.12
clpC1 4039711 p.Ile332Val missense_variant 0.13
clpC1 4039712 c.993C>T synonymous_variant 0.13
clpC1 4039715 c.990G>A synonymous_variant 0.13
clpC1 4039739 c.966C>G synonymous_variant 0.22
clpC1 4040346 p.Ala120Gly missense_variant 0.29
clpC1 4040428 p.Arg93Ser missense_variant 0.14
panD 4043981 p.Tyr101His missense_variant 0.11
embC 4242108 p.Cys749Phe missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242696 p.Leu945* stop_gained 0.17
embC 4243092 p.Leu1077Gln missense_variant 0.14
embB 4246896 p.Arg128His missense_variant 0.18
aftB 4268810 c.27G>T synonymous_variant 0.22
ubiA 4268992 p.Asp281Val missense_variant 0.15
ethR 4327303 c.-246G>T upstream_gene_variant 0.17
ethA 4327986 c.-513G>T upstream_gene_variant 0.18
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407654 c.549G>A synonymous_variant 0.14
gid 4408159 p.Arg15Leu missense_variant 0.29