TB-Profiler result

Run: ERR2229234
Summary

Run ID: ERR2229234

Sample name:

Date: 31-03-2023 16:51:12

Number of reads: 1379208

Percentage reads mapped: 89.04

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 761127 p.Ser441Ala missense_variant 0.12 rifampicin
rpoB 761196 p.Leu464Met missense_variant 0.15 rifampicin
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 7608 p.Trp103Arg missense_variant 0.14
gyrA 7777 p.Arg159Gln missense_variant 0.13
gyrA 8011 p.Ser237Phe missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576741 p.Ala465Glu missense_variant 0.14
rpoB 761132 c.1326G>C synonymous_variant 0.12
rpoB 761133 p.Leu443Met missense_variant 0.12
rpoB 761138 c.1332C>G synonymous_variant 0.15
rpoB 761150 c.1344A>C synonymous_variant 0.14
rpoB 761156 c.1350G>C synonymous_variant 0.18
rpoB 761162 c.1356G>C synonymous_variant 0.17
rpoB 761165 c.1359G>C synonymous_variant 0.12
rpoB 761174 c.1368T>C synonymous_variant 0.13
rpoB 761180 c.1374A>C synonymous_variant 0.14
rpoB 761183 c.1377T>C synonymous_variant 0.14
rpoB 761189 c.1383T>C synonymous_variant 0.14
rpoB 761193 p.Gly463Ser missense_variant 0.15
rpoB 762024 p.Val740Leu missense_variant 0.13
rpoB 762065 c.2259T>C synonymous_variant 0.12
rpoB 762080 c.2274G>C synonymous_variant 0.25
rpoB 762086 c.2280G>C synonymous_variant 0.24
rpoB 762114 p.Ile770Val missense_variant 0.16
rpoB 762156 p.Val784Ile missense_variant 0.17
rpoB 762167 c.2361T>C synonymous_variant 0.29
rpoB 762176 c.2370T>C synonymous_variant 0.19
rpoB 762180 p.Asp792Ser missense_variant 0.19
rpoB 762185 c.2379G>C synonymous_variant 0.16
rpoB 762194 c.2388G>C synonymous_variant 0.21
rpoB 762218 c.2412T>C synonymous_variant 0.19
rpoC 762887 c.-483G>C upstream_gene_variant 0.1
rpoC 762902 c.-468C>T upstream_gene_variant 0.13
rpoC 762923 c.-447C>G upstream_gene_variant 0.17
rpoC 762929 c.-441G>C upstream_gene_variant 0.21
rpoC 762959 c.-411G>C upstream_gene_variant 0.29
rpoC 762962 c.-408C>T upstream_gene_variant 0.29
rpoC 763115 c.-255T>C upstream_gene_variant 0.12
rpoB 763119 p.Asn1105Asp missense_variant 0.12
rpoC 763127 c.-243G>C upstream_gene_variant 0.12
rpoB 763130 p.Glu1108Asp missense_variant 0.11
rpoC 763133 c.-237G>C upstream_gene_variant 0.13
rpoC 763504 c.135C>A synonymous_variant 0.24
rpoC 763507 c.138G>C synonymous_variant 0.28
rpoC 763528 c.159G>C synonymous_variant 0.31
rpoC 763531 c.162G>C synonymous_variant 0.31
rpoC 763534 c.165T>C synonymous_variant 0.29
rpoC 763546 c.177A>G synonymous_variant 0.33
rpoC 763550 p.Tyr61Ala missense_variant 0.29
rpoC 763570 c.201G>C synonymous_variant 0.35
rpoC 763578 p.Phe70Tyr missense_variant 0.35
rpoC 763589 p.Ile74Val missense_variant 0.41
rpoC 763622 p.Ala85Ser missense_variant 0.36
rpoC 763630 c.261G>C synonymous_variant 0.37
rpoC 763633 c.264T>C synonymous_variant 0.35
rpoC 763636 c.267T>C synonymous_variant 0.38
rpoC 763642 c.273G>C synonymous_variant 0.31
rpoC 763647 p.Gly93Ala missense_variant 0.34
rpoC 763655 p.Glu96Lys missense_variant 0.29
rpoC 763660 c.291T>G synonymous_variant 0.25
rpoC 763666 c.297G>C synonymous_variant 0.23
rpoC 764605 c.1236G>C synonymous_variant 0.17
rpoC 764611 c.1242G>C synonymous_variant 0.17
rpoC 764620 c.1251G>C synonymous_variant 0.15
rpoC 764623 c.1254C>G synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.11
rpoC 764635 c.1266C>G synonymous_variant 0.11
rpoC 765324 p.Gly652Val missense_variant 0.18
rpoC 765691 c.2322G>T synonymous_variant 0.17
rpoC 765910 c.2541G>C synonymous_variant 0.12
rpoC 765923 p.Asn852Ala missense_variant 0.14
rpoC 765940 c.2571A>C synonymous_variant 0.14
rpoC 765947 c.2578_2580delTTGinsCTC synonymous_variant 0.13
rpoC 765962 c.2593_2595delTTGinsCTC synonymous_variant 0.18
rpoC 765970 c.2601C>G synonymous_variant 0.19
rpoC 765994 c.2625A>T synonymous_variant 0.19
rpoC 766000 c.2631G>C synonymous_variant 0.12
rpoC 766009 c.2640G>C synonymous_variant 0.11
rpoC 766366 c.2997C>A synonymous_variant 0.14
rpoC 767002 c.3633G>C synonymous_variant 0.22
rpoC 767008 c.3639G>C synonymous_variant 0.22
rpoC 767020 c.3651C>G synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777199 p.Asn428His missense_variant 0.12
mmpL5 778126 p.Asp119Tyr missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406286 p.Met352Thr missense_variant 0.12
embR 1416785 p.Ser188Ile missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.33
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.36
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.36
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.36
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.46
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.36
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.36
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.42
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.4
rrs 1472330 n.485G>T non_coding_transcript_exon_variant 0.4
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.33
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.12
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.21
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.25
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.21
rrs 1472712 n.867G>T non_coding_transcript_exon_variant 0.15
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.19
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.22
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.2
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>C non_coding_transcript_exon_variant 0.14
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.14
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.15
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.19
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.29
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.44
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.44
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.45
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.45
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.45
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.48
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.58
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.47
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.47
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.35
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.35
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.58
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.58
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.47
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.71
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.53
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.33
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.27
rrs 1473284 n.1439A>T non_coding_transcript_exon_variant 0.27
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.22
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.22
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.25
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.24
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.24
rrl 1473841 n.184A>G non_coding_transcript_exon_variant 0.25
rrl 1473969 n.312G>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474006 n.349G>T non_coding_transcript_exon_variant 0.18
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.42
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.44
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.53
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.58
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.58
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.53
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.53
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.53
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.47
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.47
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.47
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.53
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.33
rrl 1474627 n.970G>C non_coding_transcript_exon_variant 0.33
rrl 1474683 n.1026C>G non_coding_transcript_exon_variant 0.33
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.33
rrl 1474717 n.1060A>C non_coding_transcript_exon_variant 0.18
rrl 1474722 n.1065T>G non_coding_transcript_exon_variant 0.22
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.36
rrl 1474758 n.1101G>A non_coding_transcript_exon_variant 0.31
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.45
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.33
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.26
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.26
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.47
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.35
rrl 1475090 n.1433A>T non_coding_transcript_exon_variant 0.6
rrl 1475104 n.1447T>A non_coding_transcript_exon_variant 0.62
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.62
rrl 1475124 n.1467A>T non_coding_transcript_exon_variant 0.62
rrl 1475172 n.1515A>G non_coding_transcript_exon_variant 0.3
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.85
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.85
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.67
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.44
rrl 1475759 n.2102C>A non_coding_transcript_exon_variant 0.29
rrl 1475762 n.2105G>C non_coding_transcript_exon_variant 0.29
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.18
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.34
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.34
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.32
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.32
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.32
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.57
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.62
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.62
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.62
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.43
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.11
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.55
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.4
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.42
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.35
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.24
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.24
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.15
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.33
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.33
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.27
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.27
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.2
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.2
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.2
rrl 1476295 n.2638C>A non_coding_transcript_exon_variant 0.2
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.2
rrl 1476306 n.2649A>G non_coding_transcript_exon_variant 0.2
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.2
rrl 1476311 n.2654G>T non_coding_transcript_exon_variant 0.2
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.2
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.6
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.58
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.71
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.65
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.57
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.67
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.67
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.67
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.67
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.67
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.67
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.67
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.67
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.67
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.4
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.33
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.33
inhA 1674397 p.Gln66Lys missense_variant 0.25
rpsA 1833721 c.180A>G synonymous_variant 0.16
rpsA 1833727 c.186G>C synonymous_variant 0.16
rpsA 1833732 p.Pro64Leu missense_variant 0.16
rpsA 1833736 c.195C>T synonymous_variant 0.17
rpsA 1833742 c.201A>G synonymous_variant 0.17
rpsA 1833770 p.Asn77Asp missense_variant 0.25
rpsA 1833776 p.Val79Ile missense_variant 0.12
rpsA 1833992 p.Ser151Thr missense_variant 0.14
rpsA 1834093 c.552G>C synonymous_variant 0.13
rpsA 1834096 c.555G>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102403 p.Leu214Ile missense_variant 0.12
ndh 2102875 c.168C>T synonymous_variant 0.14
katG 2154041 p.Gly691Ser missense_variant 0.12
katG 2154084 c.2028G>T synonymous_variant 0.12
katG 2155380 c.732G>T synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169717 p.Asn299Ile missense_variant 0.14
PPE35 2169884 c.729T>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.45
PPE35 2170298 c.315A>G synonymous_variant 0.14
PPE35 2170372 p.Thr81Ala missense_variant 0.14
PPE35 2170400 c.213G>C synonymous_variant 0.11
PPE35 2170566 p.Phe16Tyr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289189 p.Ser18Leu missense_variant 0.11
kasA 2518363 c.249C>A synonymous_variant 0.15
kasA 2518391 p.Gln93Lys missense_variant 0.14
kasA 2518809 p.Lys232Arg missense_variant 0.29
kasA 2518864 c.750G>C synonymous_variant 0.24
kasA 2519066 p.Gly318Cys missense_variant 0.14
eis 2715055 p.Arg93Leu missense_variant 0.12
ahpC 2726638 p.Ala149Asp missense_variant 0.14
folC 2746164 p.Arg479Trp missense_variant 0.12
folC 2746843 c.756C>T synonymous_variant 0.29
folC 2747213 p.Pro129Leu missense_variant 0.13
folC 2747512 p.Gln29His missense_variant 0.15
folC 2747659 c.-61A>C upstream_gene_variant 0.17
thyA 3074580 c.-109T>C upstream_gene_variant 0.12
Rv3236c 3612804 c.312delT frameshift_variant 0.17
Rv3236c 3612877 c.240C>G synonymous_variant 0.2
fbiA 3641309 p.Ala256Gly missense_variant 0.11
fbiB 3642241 p.Gly236Val missense_variant 0.14
fbiB 3642493 p.Asp320Gly missense_variant 0.15
alr 3841025 c.396G>T synonymous_variant 0.11
rpoA 3878639 c.-132C>G upstream_gene_variant 0.4
clpC1 4039499 c.1206G>C synonymous_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039994 p.Glu237Asp missense_variant 0.12
clpC1 4040057 c.648C>T synonymous_variant 0.23
embC 4241221 c.1359C>A synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244303 p.Asn357Lys missense_variant 0.14
embB 4245824 c.-690G>A upstream_gene_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.42
embB 4246548 p.Pro12Gln missense_variant 0.23
embB 4246555 c.42G>C synonymous_variant 0.3
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.2
aftB 4268840 c.-4G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0