TB-Profiler result

Run: SRR1062873
Summary

Run ID: SRR1062873

Sample name:

Date: 02-04-2023 18:37:57

Number of reads: 2748127

Percentage reads mapped: 87.48

Strain: lineage4.6.1.2;lineage4.4.1.1

Drug-resistance: HR-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
lineage4.6 Euro-American T;LAM None 0.72
lineage4.4 Euro-American S;T None 0.26
lineage4.4.1 Euro-American (S-type) S;T None 0.27
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.67
lineage4.6.1.2 Euro-American T2 RD724 0.72
lineage4.4.1.1 Euro-American S;Orphans None 0.27
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.79 isoniazid, ethionamide
gid 4408100 c.102delG frameshift_variant 0.66 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 0.98
gyrA 7539 p.Thr80Ala missense_variant 0.68
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9276 c.1975C>T synonymous_variant 0.49
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764810 p.Pro481Thr missense_variant 0.63
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303391 p.Arg154His missense_variant 0.71
embR 1416410 p.Leu313Arg missense_variant 0.8
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.17
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.19
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.21
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.2
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.24
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.24
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.25
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.23
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.24
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.24
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.22
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.21
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.21
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.18
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.22
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.33
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.35
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.35
rrs 1472575 n.730C>T non_coding_transcript_exon_variant 0.33
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.31
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.31
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.32
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.19
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.17
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.38
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.61
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.66
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.63
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.56
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.2
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.12
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.11
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.12
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.15
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.15
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.15
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.19
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.23
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.26
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.27
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.25
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.23
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.22
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.18
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.16
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.2
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.18
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.17
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.17
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.17
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.17
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.17
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.35
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.47
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.46
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.54
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.54
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.53
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.63
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.62
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.62
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.62
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.52
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.49
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.22
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.21
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.21
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.21
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.21
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.2
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.2
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.2
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.19
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.19
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.19
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.2
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.32
katG 2154349 p.Glu588Gly missense_variant 0.2
katG 2155541 p.Trp191Gly missense_variant 0.77
PPE35 2169840 p.Gly258Asp missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746923 p.Gly226Ser missense_variant 0.27
Rv2752c 3065920 p.Pro91Leu missense_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 0.27
Rv3083 3448608 c.105G>A synonymous_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243692 p.Gly154Ser missense_variant 0.29
embA 4245055 p.Thr608Asn missense_variant 0.79
embB 4246904 p.Val131Met missense_variant 0.45
ethA 4327107 p.His123Tyr missense_variant 0.72
ethR 4328171 p.Val208Ala missense_variant 0.74
ethA 4328252 c.-779T>G upstream_gene_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0