TB-Profiler result

Run: ERR6197021
Summary

Run ID: ERR6197021

Sample name:

Date: 02-04-2023 01:49:29

Number of reads: 2482394

Percentage reads mapped: 94.98

Strain: lineage4.7;lineage4.3.4.2

Drug-resistance: MDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.45
lineage4.7 Euro-American (mainly T) T1;T5 None 0.49
lineage4.3.4 Euro-American (LAM) LAM RD174 0.48
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.49
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 761155 p.Ser450Leu missense_variant 0.34 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.75 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.81 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.59 ethambutol
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 6140 p.Val301Leu missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.28
gyrA 9304 p.Gly668Asp missense_variant 0.37
rpoC 762989 c.-381G>C upstream_gene_variant 0.14
rpoB 763005 p.Cys1067Val missense_variant 0.15
rpoC 763028 c.-342T>C upstream_gene_variant 0.11
rpoC 763053 c.-317T>C upstream_gene_variant 0.12
rpoC 763070 c.-300T>C upstream_gene_variant 0.1
rpoC 763615 c.246G>C synonymous_variant 0.16
rpoC 763620 p.Arg84Gln missense_variant 0.12
rpoC 763622 p.Ala85Ser missense_variant 0.16
rpoC 763630 c.261G>T synonymous_variant 0.12
rpoC 763633 c.264T>C synonymous_variant 0.12
rpoC 763642 c.273G>C synonymous_variant 0.17
rpoC 763660 c.291T>G synonymous_variant 0.13
rpoC 763663 c.294C>T synonymous_variant 0.13
rpoC 763666 c.297G>C synonymous_variant 0.14
rpoC 763669 c.300C>G synonymous_variant 0.15
rpoC 763672 c.303C>A synonymous_variant 0.14
rpoC 763696 c.327T>C synonymous_variant 0.14
rpoC 763699 c.330G>T synonymous_variant 0.14
rpoC 763702 c.333C>T synonymous_variant 0.12
rpoC 763705 c.336G>C synonymous_variant 0.12
rpoC 763708 c.339G>C synonymous_variant 0.13
rpoC 763714 c.345G>T synonymous_variant 0.12
rpoC 763717 c.348T>C synonymous_variant 0.15
rpoC 763720 c.351G>T synonymous_variant 0.12
rpoC 763729 c.360G>T synonymous_variant 0.12
rpoC 763732 c.363C>T synonymous_variant 0.14
rpoC 764918 p.Val517Leu missense_variant 0.5
rpoC 764995 c.1626C>G synonymous_variant 0.51
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 1.0
rrs 1471925 n.80_81insGCAGCTTG non_coding_transcript_exon_variant 1.0
rrs 1471928 n.83T>G non_coding_transcript_exon_variant 1.0
rrs 1471930 n.88_89delGA non_coding_transcript_exon_variant 1.0
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 1.0
rrs 1471978 n.133C>T non_coding_transcript_exon_variant 1.0
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.67
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.67
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.67
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.67
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.67
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 1.0
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.67
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 1.0
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 1.0
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.88
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.88
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.89
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.18
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.91
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.91
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 1.0
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 1.0
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.82
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 1.0
rrs 1473132 n.1287T>C non_coding_transcript_exon_variant 0.14
rrs 1473135 n.1290C>T non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.75
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.94
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.67
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.76
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.13
rrs 1473293 n.1448G>T non_coding_transcript_exon_variant 0.13
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.77
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.76
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.76
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 1.0
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.33
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.86
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.86
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.57
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.57
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.29
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.29
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.57
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.57
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.57
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.29
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.8
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.8
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.8
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.8
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.4
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.4
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.18
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.71
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.29
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.71
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 0.73
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 1.0
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.12
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.12
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 1.0
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.87
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.13
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.88
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.12
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.88
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.12
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.12
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.4
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.4
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.38
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.35
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.27
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.27
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.88
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.88
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 1.0
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 1.0
rpsA 1833469 c.-73G>T upstream_gene_variant 0.45
rpsA 1834249 c.708T>C synonymous_variant 0.1
rpsA 1834261 c.720A>G synonymous_variant 0.12
rpsA 1834306 c.765T>C synonymous_variant 0.11
rpsA 1834312 c.771G>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289200 c.42C>T synonymous_variant 0.51
thyA 3073868 p.Thr202Ala missense_variant 0.54
ald 3086788 c.-32T>C upstream_gene_variant 0.51
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.54
Rv3236c 3612009 p.Ala370Thr missense_variant 0.48
fbiA 3641119 p.Ser193Pro missense_variant 0.47
alr 3840719 c.702A>G synonymous_variant 0.33
rpoA 3878641 c.-135delG upstream_gene_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407970 p.Pro78Leu missense_variant 0.4
gid 4408156 p.Leu16Arg missense_variant 0.3