TB-Profiler result

Run: ERR1199057
Summary

Run ID: ERR1199057

Sample name:

Date: 14-08-2022 01:33:24

Number of reads: 6241528

Percentage reads mapped: 90.08

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 0.99
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.27 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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.98
fgd1 491313 c.531C>A synonymous_variant 0.36
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 1472150 n.305T>A non_coding_transcript_exon_variant 0.25
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.39
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.17
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.18
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.12
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.38
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.4
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.13
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.35
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.44
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.29
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.28
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.33
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.3
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.25
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.36
rrl 1475552 n.1895G>C non_coding_transcript_exon_variant 0.18
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.27
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.4
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.36
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.42
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.38
rrl 1475855 n.2198A>G non_coding_transcript_exon_variant 0.46
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.38
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.42
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.65
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154339 c.1773A>C synonymous_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986821 c.-18C>T upstream_gene_variant 0.91
ribD 2987307 p.Ala157Pro missense_variant 0.14
Rv2752c 3065279 p.Thr305Ala missense_variant 0.93
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840262 p.His387Tyr missense_variant 0.95
clpC1 4039363 p.Ala448Pro missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245092 c.1860C>T synonymous_variant 0.96
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0