TB-Profiler result

Run: ERR2229810
Summary

Run ID: ERR2229810

Sample name:

Date: 31-03-2023 17:36:18

Number of reads: 98076

Percentage reads mapped: 61.76

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 0.08
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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.75 kanamycin, capreomycin, aminoglycosides, amikacin
tlyA 1918322 c.385delG frameshift_variant 0.67 capreomycin
panD 4043900 p.Ala128Ser missense_variant 1.0 pyrazinamide
ethR 4327831 p.Ala95Thr missense_variant 0.4 ethionamide
gid 4408108 c.94delG frameshift_variant 0.29 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 5251 c.17delA frameshift_variant 0.22
gyrA 7993 p.Ala231Val missense_variant 0.33
gyrA 8211 p.Asp304Tyr missense_variant 0.29
gyrA 9639 p.Gly780Ser missense_variant 0.5
fgd1 491407 p.Pro209Thr missense_variant 0.67
mshA 575830 c.483C>A synonymous_variant 0.5
ccsA 620820 c.930T>C synonymous_variant 0.67
ccsA 620837 p.Gly316Val missense_variant 0.5
rpoB 760751 c.945G>T synonymous_variant 1.0
rpoC 762899 c.-471G>T upstream_gene_variant 1.0
rpoC 762920 c.-450C>T upstream_gene_variant 1.0
rpoC 762929 c.-441G>C upstream_gene_variant 0.5
rpoC 762959 c.-411G>T upstream_gene_variant 0.5
rpoC 762971 c.-399G>C upstream_gene_variant 0.5
rpoC 762983 c.-387C>T upstream_gene_variant 1.0
rpoC 762989 c.-381G>A upstream_gene_variant 1.0
rpoC 762995 c.-375G>T upstream_gene_variant 1.0
rpoB 763002 c.3197dupA frameshift_variant 1.0
rpoB 763006 c.3201delC frameshift_variant 1.0
rpoB 763017 p.Gln1071Glu missense_variant 0.67
rpoC 763537 c.168C>G synonymous_variant 0.5
rpoC 763546 c.177A>G synonymous_variant 1.0
rpoC 763570 c.201G>C synonymous_variant 0.57
rpoC 763573 c.204G>C synonymous_variant 0.57
rpoC 763594 c.225C>T synonymous_variant 0.44
rpoC 763622 p.Ala85Ser missense_variant 0.29
rpoC 763627 p.Lys86Asn missense_variant 0.29
rpoC 763730 p.Ala121Thr missense_variant 1.0
rpoC 765216 p.Ala616Asp missense_variant 0.5
rpoC 765844 c.2475C>A synonymous_variant 0.67
rpoC 766706 p.Glu1113Lys missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779357 p.Arg123Met missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781655 c.96T>C synonymous_variant 0.29
rpsL 781658 c.99A>G synonymous_variant 0.29
rplC 801303 c.495G>T synonymous_variant 0.25
rplC 801318 p.Met170Ile missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304238 p.Gln436His missense_variant 0.4
fbiC 1305250 p.Arg774Trp missense_variant 0.2
Rv1258c 1406242 p.Ala367Ser missense_variant 1.0
embR 1416431 p.Ala306Val missense_variant 0.29
embR 1416642 p.Ala236Ser missense_variant 1.0
atpE 1460992 c.-53A>T upstream_gene_variant 0.5
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.5
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.5
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.5
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.5
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.5
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.43
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.33
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.33
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.33
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.75
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.5
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.5
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.5
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.4
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.4
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.4
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.71
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.78
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.88
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 1.0
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 1.0
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 1.0
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.4
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 1.0
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 1.0
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 1.0
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.75
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.75
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.8
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.5
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.5
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.5
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.5
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.4
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.5
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.67
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.67
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.5
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.5
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.5
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.5
rrl 1474269 n.612C>A non_coding_transcript_exon_variant 0.5
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.67
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.5
rrl 1474287 n.631_649delCCTTTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 1.0
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 1.0
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.5
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.5
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.4
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.67
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.67
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.67
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.67
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.67
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.75
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.75
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.75
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.75
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.75
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.75
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.75
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.75
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.8
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.6
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.6
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.33
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.33
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.6
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.6
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.6
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.6
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.6
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.6
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.6
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.4
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.4
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.4
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.4
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.4
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.4
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.4
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 0.33
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.33
rrl 1475996 n.2339T>G non_coding_transcript_exon_variant 0.33
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.6
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.6
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.78
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.78
rrl 1476172 n.2515G>T non_coding_transcript_exon_variant 0.18
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.92
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.92
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.92
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.92
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.92
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.85
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.6
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.6
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 1.0
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.75
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.75
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.75
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.75
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.83
rpsA 1834024 c.483G>C synonymous_variant 0.67
rpsA 1834034 p.Ile165Val missense_variant 0.29
rpsA 1834039 c.498C>T synonymous_variant 0.29
rpsA 1834040 p.Lys167Gln missense_variant 0.29
rpsA 1834069 c.528G>C synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102084 p.Val320Gly missense_variant 0.33
katG 2154168 p.Glu648Asp missense_variant 0.33
katG 2154447 c.1665A>G synonymous_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168948 p.Leu555Phe missense_variant 0.29
PPE35 2169311 c.1302G>T synonymous_variant 0.67
PPE35 2169325 p.Gly430Cys missense_variant 0.67
PPE35 2170226 c.387C>T synonymous_variant 0.67
PPE35 2170348 p.Gln89* stop_gained 0.4
pncA 2289355 c.-114C>A upstream_gene_variant 0.25
pncA 2289487 c.-246C>A upstream_gene_variant 0.5
kasA 2518638 p.Ser175Leu missense_variant 0.5
eis 2714934 c.399C>A synonymous_variant 0.25
ahpC 2726491 p.His100Leu missense_variant 0.33
folC 2746323 p.Gly426Arg missense_variant 0.33
folC 2746357 c.1242C>A synonymous_variant 0.22
folC 2746631 p.Gly323Val missense_variant 1.0
folC 2747215 p.Glu128Asp missense_variant 0.67
pepQ 2859744 c.675G>T synonymous_variant 1.0
pepQ 2860318 p.Ser34Leu missense_variant 0.4
thyX 3067321 p.Arg209Trp missense_variant 1.0
thyX 3067629 c.316delC frameshift_variant 0.33
ald 3087187 p.Ala123Asp missense_variant 0.5
fprA 3474568 p.Pro188Thr missense_variant 0.5
whiB7 3568513 p.Ala56Glu missense_variant 1.0
fbiB 3640929 c.-606C>T upstream_gene_variant 0.67
fbiB 3640935 c.-600C>A upstream_gene_variant 0.67
fbiA 3640951 p.Gln137Lys missense_variant 0.67
fbiA 3641020 p.Val160Ile missense_variant 0.25
fbiB 3641539 p.Thr2Asn missense_variant 0.67
alr 3841443 c.-23G>A upstream_gene_variant 0.2
alr 3841454 c.-34C>A upstream_gene_variant 0.15
rpoA 3877816 p.Gly231Val missense_variant 0.67
rpoA 3877863 c.645G>A synonymous_variant 0.4
embC 4240256 p.Leu132Ile missense_variant 0.29
embC 4241891 p.Ala677Ser missense_variant 0.33
embC 4242426 p.Arg855Leu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242676 c.-557C>T upstream_gene_variant 1.0
embA 4243265 c.33G>T synonymous_variant 0.4
embA 4243616 c.384C>A synonymous_variant 0.67
embA 4243717 p.Leu162Gln missense_variant 0.5
embA 4244206 p.Arg325Leu missense_variant 0.5
embB 4249092 p.Ser860* stop_gained 0.67
aftB 4268531 c.306C>T synonymous_variant 0.2
aftB 4268976 c.-140G>T upstream_gene_variant 0.29
ethA 4326677 p.Ser266Ile missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0