TB-Profiler result

Run: SRR6045222
Summary

Run ID: SRR6045222

Sample name:

Date: 04-04-2023 11:54:59

Number of reads: 628357

Percentage reads mapped: 27.75

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.8 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 5877 p.Val213Glu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7379 c.78C>T synonymous_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8357 c.1056G>T synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9673 p.Val791Asp missense_variant 0.29
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619783 c.-108C>T upstream_gene_variant 0.15
ccsA 620351 p.Arg154His missense_variant 0.17
ccsA 620532 c.642T>G synonymous_variant 0.3
rpoB 759620 c.-187A>C upstream_gene_variant 0.22
rpoB 759895 p.Pro30Leu missense_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760850 c.1044G>A synonymous_variant 0.11
rpoB 762534 p.Ile910Val missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767062 c.3693C>T synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.2
mmpL5 777769 p.Leu238Phe missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406525 c.816G>A synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471866 n.21C>T non_coding_transcript_exon_variant 0.25
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.29
rrs 1471911 n.66C>A non_coding_transcript_exon_variant 0.29
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.71
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.29
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.71
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.71
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.29
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.29
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.29
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.71
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.71
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.71
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.71
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.83
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.83
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.14
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.83
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.75
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.67
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.67
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.67
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 1.0
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 1.0
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 1.0
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.67
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.67
rrs 1472525 n.680C>T non_coding_transcript_exon_variant 0.12
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.67
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.68
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.74
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.74
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.15
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.8
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.81
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.78
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.72
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.86
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.86
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.89
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 1.0
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 1.0
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 1.0
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 1.0
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.89
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.89
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.81
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.82
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.69
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.21
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.64
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.56
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.25
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.25
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.5
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.75
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.38
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.2
rrs 1473017 n.1172A>G non_coding_transcript_exon_variant 0.15
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.85
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.38
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.33
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.9
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.3
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.75
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.4
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.8
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.83
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.75
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.67
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.57
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.57
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.25
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.31
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.18
rrs 1473201 n.1356delA non_coding_transcript_exon_variant 0.2
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.17
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.38
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.33
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.5
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.4
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.5
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.67
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 1.0
rrl 1474393 n.736A>G non_coding_transcript_exon_variant 1.0
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.71
rrl 1474774 n.1117A>G non_coding_transcript_exon_variant 0.29
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.29
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.29
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.29
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.8
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 1.0
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.4
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.75
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 1.0
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.5
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.56
rrl 1475794 n.2137A>G non_coding_transcript_exon_variant 0.17
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.75
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.75
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.6
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.62
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.15
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.3
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.33
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.5
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.4
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.2
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.3
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.6
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.5
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.2
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.4
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.6
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.38
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.5
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.5
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.5
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 1.0
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.75
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.75
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.75
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.8
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.9
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.82
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.91
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 1.0
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 1.0
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 1.0
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 1.0
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 1.0
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 1.0
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.92
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.92
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.94
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.96
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.96
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.96
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.92
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.92
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.97
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.97
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.95
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.85
inhA 1673529 c.-673G>A upstream_gene_variant 0.17
inhA 1674495 p.Met98Ile missense_variant 0.25
rpsA 1834306 c.765T>C synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918686 c.747G>C synonymous_variant 0.14
ndh 2101885 p.Glu386Asp missense_variant 0.11
ndh 2102506 c.537C>T synonymous_variant 1.0
ndh 2103001 p.Arg14Ser missense_variant 0.12
katG 2154958 p.Arg385Gln missense_variant 0.18
PPE35 2168461 c.2151delC frameshift_variant 0.14
Rv1979c 2221864 p.Tyr434Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288880 p.Arg121Leu missense_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715093 c.240C>T synonymous_variant 0.13
eis 2715140 p.Met65Val missense_variant 0.13
folC 2746898 p.Ile234Thr missense_variant 0.2
folC 2747371 c.228C>T synonymous_variant 0.2
pepQ 2860099 p.Leu107Pro missense_variant 0.11
ribD 2987164 p.Arg109Leu missense_variant 0.12
ribD 2987184 p.Gln116Lys missense_variant 0.15
Rv2752c 3064647 c.1545G>T synonymous_variant 0.12
Rv2752c 3064982 p.Arg404Cys missense_variant 0.12
thyX 3067714 p.Val78Leu missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087247 p.Gln143Pro missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474319 p.Gly105Arg missense_variant 0.18
Rv3236c 3612714 p.Arg135Trp missense_variant 0.2
Rv3236c 3613011 p.Tyr36His missense_variant 0.13
fbiB 3641370 c.-165C>T upstream_gene_variant 0.17
fbiB 3641777 c.243G>A synonymous_variant 0.14
fbiB 3641950 p.Arg139Gln missense_variant 0.4
fbiB 3642412 p.Arg293Gln missense_variant 0.33
alr 3841546 c.-126C>A upstream_gene_variant 0.12
ddn 3986714 c.-129delA upstream_gene_variant 0.15
clpC1 4038752 p.Gln651His missense_variant 0.11
clpC1 4039044 p.Pro554Leu missense_variant 0.12
clpC1 4040014 p.Gln231Lys missense_variant 0.22
embC 4240265 p.Arg135Ser missense_variant 0.22
embC 4240989 p.Ala376Glu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245344 c.2112G>T synonymous_variant 0.13
embA 4245786 p.Ala852Thr missense_variant 1.0
embB 4246637 p.Val42Leu missense_variant 0.25
embB 4249492 c.2979C>T synonymous_variant 0.12
aftB 4269192 c.-356C>A upstream_gene_variant 0.17
ethA 4327547 c.-74C>T upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0