TB-Profiler result

Run: SRR5818670
Summary

Run ID: SRR5818670

Sample name:

Date: 04-04-2023 11:41:51

Number of reads: 1465713

Percentage reads mapped: 84.07

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu 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 1472507 n.662C>G non_coding_transcript_exon_variant 0.14
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.16
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.16
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.2
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.2
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.25
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.25
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.28
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.27
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.23
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.29
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.31
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.31
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.38
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.31
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.31
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.31
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.14
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.14
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.13
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.12
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.12
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.14
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.11
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.15
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.11
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.12
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.15
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.19
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.11
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.12
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.15
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.12
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.12
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.11
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.11
rrl 1474722 n.1065T>A non_coding_transcript_exon_variant 0.2
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.12
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.12
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.11
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.15
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.23
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.25
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.23
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.17
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.14
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.27
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.27
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.13
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.15
rrl 1475938 n.2281C>A non_coding_transcript_exon_variant 0.12
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.14
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.14
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.14
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.13
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.13
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.15
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.14
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.14
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.16
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.16
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.16
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.23
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.27
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.24
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.28
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.3
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.26
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.26
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.26
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.27
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.26
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.23
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.26
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.29
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.29
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.37
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.41
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.45
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.45
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.45
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.46
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.46
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.38
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.49
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.49
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.11
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.36
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.11
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T 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 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4328094 c.-621C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0