TB-Profiler result

Run: ERR2229337
Summary

Run ID: ERR2229337

Sample name:

Date: 31-03-2023 17:02:13

Number of reads: 721600

Percentage reads mapped: 71.87

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 1472733 n.888G>A non_coding_transcript_exon_variant 0.31 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490915 p.Arg45Ser missense_variant 0.12
mshA 575191 c.-157C>A upstream_gene_variant 0.13
mshA 576663 p.Ala439Val missense_variant 0.12
mshA 576750 p.Lys468Thr missense_variant 0.15
rpoB 761153 c.1347G>A synonymous_variant 0.17
rpoC 762524 c.-846G>A upstream_gene_variant 0.13
rpoC 766866 p.Thr1166Asn missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775939 p.Ala848Ser missense_variant 0.12
mmpL5 777167 p.Phe438Leu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407517 c.-177G>T upstream_gene_variant 0.12
atpE 1460902 c.-143A>G upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.39
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.52
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.52
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.56
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.56
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.57
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.56
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.56
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.52
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.52
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.5
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.5
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.47
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.44
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.44
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.47
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.4
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.4
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.4
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.27
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.14
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.11
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.28
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.28
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.29
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.3
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.3
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.3
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.32
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.32
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.32
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.32
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.32
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.32
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.48
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.46
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.41
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.33
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.33
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.33
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.33
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.3
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.3
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.27
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.28
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.29
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.21
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.12
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.33
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.28
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.28
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.29
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.29
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.3
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.3
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.31
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.28
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.28
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.29
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.29
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.32
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.29
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.3
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.31
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.29
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.29
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.28
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.15
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.15
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.15
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.13
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.12
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.36
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.36
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.33
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.26
rrl 1476087 n.2430C>A non_coding_transcript_exon_variant 0.18
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.56
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.59
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.3
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.72
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.74
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.74
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.74
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.77
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.77
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.66
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.66
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.66
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.66
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.66
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.66
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.66
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.67
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.67
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.67
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.72
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.74
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.73
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.76
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.75
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.73
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.73
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.77
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.76
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.76
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.76
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.75
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.74
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.73
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.65
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.62
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.62
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.6
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.6
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.58
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.58
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.56
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.56
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.56
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.59
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.58
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.55
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.53
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.41
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.11
inhA 1674505 p.Gly102Trp missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102015 p.Val343Asp missense_variant 0.14
katG 2155813 p.Pro100Leu missense_variant 0.12
PPE35 2168334 p.Ser760Ile missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169188 c.1425C>T synonymous_variant 0.29
Rv1979c 2223157 p.Gly3Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289901 c.-660G>T upstream_gene_variant 0.14
kasA 2519224 c.1110C>A synonymous_variant 0.29
folC 2747574 p.Pro9Thr missense_variant 0.12
fbiD 3339357 c.240G>T synonymous_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
whiB7 3568683 c.-4G>T upstream_gene_variant 0.12
Rv3236c 3612553 c.564G>T synonymous_variant 0.12
fbiA 3640723 p.Asp61Tyr missense_variant 0.12
panD 4044117 c.165G>T synonymous_variant 0.14
embC 4241981 p.Pro707Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242854 p.Gly998Cys missense_variant 0.13
embA 4244851 p.Arg540Leu missense_variant 0.15
embB 4247318 p.Ile269Phe missense_variant 0.11
embB 4249733 p.Pro1074Thr missense_variant 0.25
aftB 4268267 c.570G>T synonymous_variant 0.13
aftB 4268726 c.111G>T synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0