TB-Profiler result

Run: ERR6197023
Summary

Run ID: ERR6197023

Sample name:

Date: 02-04-2023 01:49:38

Number of reads: 2545384

Percentage reads mapped: 95.54

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 0.13
lineage4.7 Euro-American (mainly T) T1;T5 None 0.82
lineage4.3.4 Euro-American (LAM) LAM RD174 0.11
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.15
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 0.22 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.73 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.69 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.19 isoniazid
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
rpoB 759615 c.-192A>C upstream_gene_variant 0.29
rpoC 762989 c.-381G>C upstream_gene_variant 0.15
rpoB 763005 p.Cys1067Val missense_variant 0.14
rpoC 763028 c.-342T>C upstream_gene_variant 0.12
rpoC 763053 c.-317T>C upstream_gene_variant 0.14
rpoC 763070 c.-300T>C upstream_gene_variant 0.11
rpoC 763578 p.Phe70Tyr missense_variant 0.12
rpoC 763666 c.297G>C synonymous_variant 0.12
rpoC 764918 p.Val517Leu missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302815 c.-116G>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.67
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472620 n.775A>C non_coding_transcript_exon_variant 0.5
rrs 1472634 n.789T>G non_coding_transcript_exon_variant 0.5
rrs 1472647 n.802C>A non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 1.0
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472733 n.888G>T non_coding_transcript_exon_variant 0.33
rrs 1472734 n.889C>A non_coding_transcript_exon_variant 0.33
rrs 1472741 n.896G>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.33
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.33
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.33
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.33
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.8
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.8
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 1.0
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 1.0
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 1.0
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 1473252 n.1407T>C non_coding_transcript_exon_variant 0.77
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.9
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.72
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.74
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.14
rrs 1473293 n.1448G>T non_coding_transcript_exon_variant 0.14
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.75
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.72
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.74
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.6
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 0.8
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.9
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.8
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.8
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.9
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.9
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 0.8
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.88
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 1.0
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.93
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.93
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.93
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.93
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.27
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.27
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.2
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.27
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.38
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.43
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.57
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.43
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 1.0
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 1.0
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.43
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.75
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.75
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 1.0
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 1.0
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 1.0
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 1.0
rpsA 1833424 c.-118C>T upstream_gene_variant 0.12
rpsA 1833469 c.-73G>T upstream_gene_variant 0.29
rpsA 1834306 c.765T>C synonymous_variant 0.11
rpsA 1834327 c.786G>T 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 0.89
thyA 3073868 p.Thr202Ala missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.11
alr 3840719 c.702A>G synonymous_variant 0.19
clpC1 4038287 c.2418C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 0.74
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407970 p.Pro78Leu missense_variant 0.14
gid 4408156 p.Leu16Arg missense_variant 0.17