TB-Profiler result

Run: SRR10315462
Summary

Run ID: SRR10315462

Sample name:

Date: 02-04-2023 17:06:22

Number of reads: 5713282

Percentage reads mapped: 91.67

Strain: lineage4.3.2.1

Drug-resistance: RR-TB

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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
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.15 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.75 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.23
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777886 p.Ala199Thr 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 1472217 n.372A>G non_coding_transcript_exon_variant 0.29
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.23
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.23
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.23
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.27
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.29
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.29
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.29
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.33
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.42
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.42
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.42
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.38
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.38
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.46
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.5
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.36
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.36
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.38
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.38
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.3
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.33
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.33
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.43
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.5
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.25
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.75
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.86
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.6
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.17
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.21
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.21
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.21
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.21
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.27
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.27
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.3
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.3
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.42
rrs 1473047 n.1202C>T non_coding_transcript_exon_variant 0.2
rrs 1473052 n.1207G>A non_coding_transcript_exon_variant 0.22
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.33
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.33
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.33
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.3
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.27
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.32
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.27
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.26
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.26
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.24
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.22
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.2
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrl 1475834 n.2177T>C non_coding_transcript_exon_variant 0.25
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.22
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.22
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.22
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.25
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.4
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.33
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.43
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.43
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.38
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.38
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.38
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.38
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.38
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.38
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.38
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.33
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.33
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.33
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.23
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.35
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.48
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.46
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.48
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.43
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.56
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.47
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.44
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.12
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.12
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.12
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.12
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.12
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.19
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.19
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.24
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.12
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G 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 0.99
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0