TB-Profiler result

Run: ERR2229332
Summary

Run ID: ERR2229332

Sample name:

Date: 31-03-2023 17:01:42

Number of reads: 711598

Percentage reads mapped: 85.14

Strain: lineage4.8

Drug-resistance: RR-TB

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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
rpoB 761140 p.His445Leu missense_variant 0.12 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.36 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
gyrA 8669 c.1368C>A synonymous_variant 0.17
gyrA 8802 p.Ala501Thr missense_variant 0.14
gyrA 9287 c.1986G>T synonymous_variant 0.18
gyrA 9621 c.2320C>T synonymous_variant 0.12
gyrA 9791 c.2490C>T synonymous_variant 0.13
fgd1 491311 p.Gly177Ser missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576111 p.Ala255Gly missense_variant 0.29
rpoC 765959 p.Ala864Thr missense_variant 0.18
rpoC 766711 c.3342C>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778226 c.-764T>C upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800829 c.21C>T synonymous_variant 0.2
fbiC 1303135 p.Gly69Cys missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304673 c.1743C>T synonymous_variant 0.14
fbiC 1304985 c.2055G>T synonymous_variant 0.33
Rv1258c 1407039 p.Val101Asp missense_variant 0.22
embR 1417254 p.Thr32Ala missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.21
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.2
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.17
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.16
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.19
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.16
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.16
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.16
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.12
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.16
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.2
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.2
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.19
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.19
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.19
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.21
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.39
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.42
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.37
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.36
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.39
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.37
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.32
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.36
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.12
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.12
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.25
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.18
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.17
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.16
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.16
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.26
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.26
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.41
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.17
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.17
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.17
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.18
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.18
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.29
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.26
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.26
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 0.14
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.14
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.14
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.14
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.14
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.16
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.16
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.33
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.33
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.15
rrl 1474255 n.598C>T non_coding_transcript_exon_variant 0.14
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.16
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.11
rrl 1474447 n.790G>T non_coding_transcript_exon_variant 0.14
rrl 1474524 n.867C>G non_coding_transcript_exon_variant 0.15
rrl 1475163 n.1506T>G non_coding_transcript_exon_variant 0.17
rrl 1475299 n.1642G>T non_coding_transcript_exon_variant 0.18
rrl 1475498 n.1841C>G non_coding_transcript_exon_variant 0.15
rrl 1475514 n.1857G>A non_coding_transcript_exon_variant 0.12
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.12
rrl 1475529 n.1872A>T non_coding_transcript_exon_variant 0.12
rrl 1475539 n.1882A>G non_coding_transcript_exon_variant 0.11
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.17
rrl 1475552 n.1895G>C non_coding_transcript_exon_variant 0.14
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.13
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.17
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.17
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.27
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.3
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.32
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.28
rrl 1475895 n.2238C>G non_coding_transcript_exon_variant 0.25
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.28
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.18
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.43
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.53
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.27
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.21
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.2
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.21
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.2
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.19
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.19
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.19
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.19
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.18
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.16
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.16
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.26
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.51
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.49
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.46
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.39
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.39
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.43
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.4
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.48
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.3
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.28
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.24
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.25
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.25
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.25
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.26
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.26
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.26
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.26
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.25
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.25
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.23
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rrl 1476659 n.3002A>G non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
fabG1 1673860 p.Val141Ile missense_variant 0.14
rpsA 1834273 p.His244Gln missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102093 p.Val317Ala missense_variant 0.12
ndh 2102268 p.Val259Ile missense_variant 0.25
katG 2154317 p.Gly599Arg missense_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.31
PPE35 2167868 c.2745A>C synonymous_variant 0.33
PPE35 2167878 p.Ser912Asn missense_variant 0.2
PPE35 2167898 c.2715G>C synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169351 p.Ala421Phe missense_variant 0.14
PPE35 2169890 c.723C>T synonymous_variant 0.15
PPE35 2169893 c.720C>A synonymous_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.52
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289500 c.-260delG upstream_gene_variant 0.14
kasA 2518171 c.57C>A synonymous_variant 0.17
folC 2746898 p.Ile234Asn missense_variant 0.15
pepQ 2859305 p.Leu372Met missense_variant 0.15
ribD 2986658 c.-180delG upstream_gene_variant 0.15
Rv2752c 3065086 p.Arg369Met missense_variant 0.13
thyX 3068049 c.-104C>G upstream_gene_variant 0.14
thyA 3073716 p.Asp252Glu missense_variant 0.18
thyA 3074279 p.Gly65Ser missense_variant 0.17
thyA 3074318 p.Phe52Leu missense_variant 0.12
fbiD 3339589 p.Leu158Val missense_variant 0.14
fbiD 3339640 p.Ala175Ser missense_variant 0.17
Rv3083 3448460 c.-44C>A upstream_gene_variant 0.29
whiB7 3568488 c.192C>A synonymous_variant 0.15
whiB7 3568794 c.-115C>T upstream_gene_variant 0.12
Rv3236c 3612255 p.Val288Phe missense_variant 0.4
Rv3236c 3612816 p.Ala101Thr missense_variant 0.4
Rv3236c 3613170 c.-54G>A upstream_gene_variant 0.17
fbiA 3641237 p.Ala232Glu missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.32
rpoA 3877622 p.Glu296* stop_gained 0.14
clpC1 4039691 c.1014G>C synonymous_variant 0.11
clpC1 4039829 p.Leu292Phe missense_variant 0.15
embC 4240625 p.Asp255Tyr missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245641 p.Asn803Lys missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.73
embB 4246556 p.Ala15Pro missense_variant 0.73
embB 4246563 p.Leu17Trp missense_variant 0.43
aftB 4267107 p.Ser577Cys missense_variant 0.12
aftB 4268318 c.519C>A synonymous_variant 0.13
aftB 4269240 c.-404G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0