TB-Profiler result

Run: SRR6153166
Summary

Run ID: SRR6153166

Sample name:

Date: 19-10-2023 10:54:13

Number of reads: 5491570

Percentage reads mapped: 96.3

Strain: lineage1.2.1.2.1

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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rrs n.888G>A (0.44)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1402C>A (0.16)
Amikacin R rrs n.1402C>A (0.16)
Capreomycin R rrs n.1402C>A (0.16)
Kanamycin R rrs n.1402C>A (0.16)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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 0.44 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.16 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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.14
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.24
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.18
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.18
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.15
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.16
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.19
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.32
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.35
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.34
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.33
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.41
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.43
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.28
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.21
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.55
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.46
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.45
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.26
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.55
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.48
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.48
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.49
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 0.41
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.45
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.45
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.47
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.42
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.49
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.44
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.52
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.41
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.42
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.26
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.3
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.25
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.25
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.26
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.26
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.24
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.22
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.18
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.23
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.22
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.24
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.28
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.15
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.16
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.25
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.26
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.17
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.22
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.2
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.19
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.74
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.27
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.28
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.32
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.26
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.42
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.33
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.33
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.32
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.39
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.34
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.41
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.34
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.39
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.34
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.34
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.18
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.16
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.12
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.23
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.24
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.2
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.25
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.19
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.2
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.19
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.21
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.25
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.23
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.19
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.24
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.23
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.26
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.21
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.18
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.21
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.27
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.26
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.25
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.4
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.44
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.44
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.54
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.55
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.56
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.56
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.6
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.69
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.55
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.41
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.16
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.16
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.14
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.16
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.23
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.13
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0