TB-Profiler result

Run: ERR216901
Summary

Run ID: ERR216901

Sample name:

Date: 31-03-2023 15:55:04

Number of reads: 923929

Percentage reads mapped: 11.01

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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 0.71 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8941 p.Ala547Val missense_variant 0.12
gyrA 9059 c.1758G>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766904 p.Ser1179Thr missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777160 p.Ala441Thr missense_variant 0.13
mmpR5 779392 p.Arg135Trp missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303656 c.726G>A synonymous_variant 0.13
Rv1258c 1406767 p.Gln192Lys missense_variant 0.12
embR 1417527 c.-180A>G upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.18
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.27
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.39
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.63
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.64
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.72
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.83
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.83
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.85
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.86
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.87
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.88
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.8
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.8
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.8
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.77
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.7
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.67
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.66
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.37
rrs 1472282 n.437T>G non_coding_transcript_exon_variant 0.12
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.16
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.3
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.45
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.44
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.43
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.43
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.43
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.45
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.45
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.47
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.46
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.47
rrs 1472600 n.755C>T non_coding_transcript_exon_variant 0.45
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.47
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.2
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.3
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.71
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.72
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.73
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.73
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.73
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.72
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.27
rrs 1472990 n.1145A>T non_coding_transcript_exon_variant 0.12
rrs 1473000 n.1155G>C non_coding_transcript_exon_variant 0.46
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.44
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.47
rrs 1473010 n.1165C>G non_coding_transcript_exon_variant 0.47
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.4
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.39
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.4
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.42
rrs 1473080 n.1235C>G non_coding_transcript_exon_variant 0.44
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.44
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.15
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.18
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.22
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.22
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.21
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.21
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.19
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.19
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.19
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.18
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.36
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.4
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.62
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.67
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.71
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.82
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.81
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.85
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.85
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.85
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.82
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.79
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.79
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.77
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.75
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.75
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.75
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.74
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.72
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.69
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.64
rrl 1476573 n.2916A>G non_coding_transcript_exon_variant 0.62
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.51
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.32
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.28
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.26
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.26
rrl 1476621 n.2964C>T non_coding_transcript_exon_variant 0.26
rrl 1476624 n.2967T>C non_coding_transcript_exon_variant 0.26
rrl 1476625 n.2968C>A non_coding_transcript_exon_variant 0.26
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.26
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.25
rrl 1476637 n.2980C>A non_coding_transcript_exon_variant 0.25
rrl 1476657 n.3000G>T non_coding_transcript_exon_variant 0.14
inhA 1673718 c.-484G>C upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.34
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518731 p.Pro206His missense_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.36
ahpC 2726586 p.Asp132His missense_variant 0.13
folC 2746605 p.Ala332Thr missense_variant 0.25
pepQ 2860137 p.Lys94Asn missense_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.2
thyA 3073806 c.666C>G synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840544 p.Val293Met missense_variant 0.2
rpoA 3878569 c.-62C>G upstream_gene_variant 0.18
clpC1 4038857 c.1848C>A synonymous_variant 0.18
clpC1 4040016 p.Ala230Val missense_variant 0.12
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.19
embA 4242853 c.-380C>T upstream_gene_variant 0.12
embB 4247080 c.567C>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0