TB-Profiler result

Run: SRR1173404
Summary

Run ID: SRR1173404

Sample name:

Date: 03-04-2023 03:24:10

Number of reads: 1297265

Percentage reads mapped: 91.3

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 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
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 1472557 n.712G>A non_coding_transcript_exon_variant 0.11
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.1
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.1
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.1
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.12
rrl 1474790 n.1133C>T 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 0.17
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.12
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.11
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.12
rrl 1475855 n.2198A>G non_coding_transcript_exon_variant 0.69
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.11
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.11
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.11
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.18
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.31
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.32
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.32
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.39
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.4
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.37
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154339 c.1773A>C synonymous_variant 0.74
PPE35 2169320 p.Leu431Phe missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986821 c.-18C>T upstream_gene_variant 0.69
ribD 2987597 c.759C>G synonymous_variant 0.12
Rv2752c 3065279 p.Thr305Ala missense_variant 0.62
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840262 p.His387Tyr missense_variant 0.81
alr 3840900 p.Ala174Asp missense_variant 0.14
clpC1 4039070 c.1635G>T synonymous_variant 0.11
panD 4043882 p.Pro134Ser missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244057 c.825C>A synonymous_variant 0.11
embA 4244262 p.Leu344Met missense_variant 0.12
embA 4245092 c.1860C>T synonymous_variant 0.84
aftB 4267601 c.1236C>A synonymous_variant 0.11
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0