TB-Profiler result

Run: SRR6046016
Summary

Run ID: SRR6046016

Sample name:

Date: 04-04-2023 12:09:33

Number of reads: 1860316

Percentage reads mapped: 95.76

Strain: lineage4.3.1.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.1 Euro-American (LAM) LAM9 None 1.0
lineage4.3.1.1 Euro-American (LAM) LAM9 None 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.21 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_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 1471660 n.-186G>A upstream_gene_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.25
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.4
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.4
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.35
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.12
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.29
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.18
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.22
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.22
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.22
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.3
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.1
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.24
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.24
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.18
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.18
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.17
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.13
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.11
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.12
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.4
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.33
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.43
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.25
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.25
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.25
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.25
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.25
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.25
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.25
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.23
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.27
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.21
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.25
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.25
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.27
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.25
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.24
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.24
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.18
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.2
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.2
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.23
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.21
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.21
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.23
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.17
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>T 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 0.17
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.2
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.18
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.36
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.41
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.48
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.46
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.48
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.45
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.45
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.28
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.42
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.48
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.26
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067966 c.-21G>A upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0