TB-Profiler result

Run: ERR1199021
Summary

Run ID: ERR1199021

Sample name:

Date: 15-08-2022 10:16:54

Number of reads: 14015134

Percentage reads mapped: 67.57

Strain: lineage4.6.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.1 Euro-American T2-Uganda RD724 1.0
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
ethA 4326008 c.1465delG frameshift_variant 1.0 ethionamide
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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
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 1471896 n.51T>C non_coding_transcript_exon_variant 0.34
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.33
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.34
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.36
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.22
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.16
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.51
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.5
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.49
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.22
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.19
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.3
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.34
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.4
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.49
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.62
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.51
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.34
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.31
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.23
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.16
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.13
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.22
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.12
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.15
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.15
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.15
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.22
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.34
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.35
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.16
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.16
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.1
rrl 1475552 n.1895G>C non_coding_transcript_exon_variant 0.15
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.15
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.17
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.34
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.34
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.27
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.17
rrl 1475871 n.2214T>C non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.41
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.36
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.39
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.4
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.42
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.54
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.54
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.8
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.62
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.58
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.56
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.58
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.59
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.19
PPE35 2169866 c.747G>C synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.13
thyA 3073806 c.666C>G synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640981 p.Asp147Asn missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.23
clpC1 4039363 p.Ala448Pro missense_variant 0.2
embC 4239842 c.-21C>A upstream_gene_variant 0.17
embC 4242425 p.Arg855Gly missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.26
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407596 p.Val203Met missense_variant 0.99