TB-Profiler result

Run: ERR4820624
Summary

Run ID: ERR4820624

Sample name:

Date: 01-04-2023 16:47:04

Number of reads: 853456

Percentage reads mapped: 95.55

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 0.99
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 1472733 n.888G>A non_coding_transcript_exon_variant 0.69 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.4 kanamycin, capreomycin, aminoglycosides, amikacin
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 7979 c.678G>A synonymous_variant 0.18
rpoC 767287 c.3918G>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.33
fbiC 1303637 p.Lys236Arg missense_variant 0.14
atpE 1461083 c.39T>A synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.5
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.5
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.5
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.75
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.75
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.85
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.85
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.87
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.87
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.87
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.93
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.93
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.93
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.89
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.89
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.75
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.67
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.5
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.5
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.5
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.33
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.6
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.5
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.33
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.5
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.5
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.44
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.64
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.18
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.64
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.64
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.64
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.8
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.78
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.78
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.2
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.2
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.22
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.27
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.25
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.14
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.14
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.14
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.15
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.15
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.46
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.6
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.67
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.67
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.33
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.67
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.5
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.5
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.5
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.4
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.6
rrl 1473495 n.-163T>C upstream_gene_variant 0.22
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.5
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.33
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.6
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.75
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rpsA 1833910 p.Asp123Glu missense_variant 1.0
rpsA 1833933 p.Ile131Asn missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102875 c.168C>T synonymous_variant 0.11
katG 2154251 p.Ala621Thr missense_variant 0.12
katG 2154650 p.Lys488Glu missense_variant 0.1
PPE35 2167669 p.Phe982Leu missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288762 c.480A>G synonymous_variant 0.12
kasA 2518151 p.Ser13Arg missense_variant 0.25
kasA 2518269 p.Thr52Asn missense_variant 0.11
ahpC 2726301 p.Thr37Ala missense_variant 0.11
ahpC 2726414 p.Glu74Asp missense_variant 0.12
ald 3087652 p.Ser278* stop_gained 0.1
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612997 c.120T>G synonymous_variant 0.18
alr 3840436 c.985C>T synonymous_variant 0.11
clpC1 4039645 p.His354Asp missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249330 p.Met939Ile missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0