TB-Profiler result

Run: SRR1173835
Summary

Run ID: SRR1173835

Sample name:

Date: 03-04-2023 03:32:37

Number of reads: 994110

Percentage reads mapped: 90.73

Strain: lineage4.6.1.1

Drug-resistance: Sensitive

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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
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 8789 c.1488C>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576711 p.Arg455Gln missense_variant 0.29
rpoB 761757 p.Tyr651His missense_variant 0.12
rpoC 763019 c.-351G>A upstream_gene_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406823 p.Thr173Lys missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1475855 n.2198A>G non_coding_transcript_exon_variant 0.68
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.19
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.24
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.26
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.29
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.3
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.26
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.19
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.24
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.19
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102475 p.Ala190Ser missense_variant 0.12
katG 2154339 c.1773A>C synonymous_variant 0.81
katG 2154417 c.1695G>T synonymous_variant 0.13
katG 2156091 c.21C>A synonymous_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859464 p.Gly319Cys missense_variant 0.11
pepQ 2860591 c.-173C>A upstream_gene_variant 0.11
ribD 2986821 c.-18C>T upstream_gene_variant 0.71
Rv2752c 3065279 p.Thr305Ala missense_variant 0.65
ald 3087066 p.Gly83Arg missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840262 p.His387Tyr missense_variant 0.36
clpC1 4040072 c.633C>T synonymous_variant 0.12
panD 4043882 p.Pro134Ser missense_variant 0.21
embC 4240357 c.495C>G synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245092 c.1860C>T synonymous_variant 0.85
embB 4247950 c.1437G>A synonymous_variant 0.2
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338567 c.-46C>T upstream_gene_variant 0.12
whiB6 4338594 c.-75delG upstream_gene_variant 1.0
gid 4408102 p.Gly34Val missense_variant 0.12