TB-Profiler result

Run: SRR5818684
Summary

Run ID: SRR5818684

Sample name:

Date: 04-04-2023 11:42:22

Number of reads: 2621396

Percentage reads mapped: 87.82

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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 0.11 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.18 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.13 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 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A 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 1472558 n.713G>A non_coding_transcript_exon_variant 0.12
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.13
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.12
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.13
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.12
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.13
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.11
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.13
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.13
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.14
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.13
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.1
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.13
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.11
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.15
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.14
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.1
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.14
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.14
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.12
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.1
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.28
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.14
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.18
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.18
rrl 1475990 n.2333G>A non_coding_transcript_exon_variant 0.14
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.17
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.14
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.14
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.17
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.1
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.1
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.31
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.17
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.12
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.18
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.18
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.23
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.13
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.21
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.13
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.16
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.19
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.21
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.28
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.22
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.19
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.31
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0