TB-Profiler result

Run: SRR6046736
Summary

Run ID: SRR6046736

Sample name:

Date: 20-10-2023 18:11:21

Number of reads: 2442645

Percentage reads mapped: 98.01

Strain: lineage2.2.1;La3

Drug-resistance: Sensitive

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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
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
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
La3 M.orygis None None 0.66
lineage2 East-Asian Beijing RD105 0.24
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.25
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.23
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
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 5516 p.Ile93Val missense_variant 0.77
gyrB 5920 c.681C>T synonymous_variant 0.79
gyrB 6109 c.870G>A synonymous_variant 0.79
gyrB 6446 p.Ala403Ser missense_variant 0.8
gyrB 6717 p.Ile493Thr missense_variant 0.78
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8930 c.1629C>T synonymous_variant 0.7
gyrA 9143 c.1842T>C synonymous_variant 0.72
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 0.85
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491749 p.Leu323Phe missense_variant 0.78
mshA 575907 p.Ala187Val missense_variant 0.3
ccsA 620625 p.Ile245Met missense_variant 0.25
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.23
mmpL5 778086 c.394dupG frameshift_variant 0.73
mmpS5 778588 p.Gln106His missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.76
Rv1258c 1406760 c.580_581insC frameshift_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475539 n.1882A>G non_coding_transcript_exon_variant 0.75
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.2
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476664 n.3007T>G non_coding_transcript_exon_variant 0.71
inhA 1673680 c.-522C>G upstream_gene_variant 0.69
rpsA 1834177 c.636A>C synonymous_variant 0.29
rpsA 1834363 c.822G>A synonymous_variant 0.65
rpsA 1834433 p.Pro298Ser missense_variant 0.69
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154707 p.Val469Leu missense_variant 0.81
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 0.68
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 0.81
PPE35 2170669 c.-57G>A upstream_gene_variant 0.79
Rv1979c 2222308 p.Asp286Gly missense_variant 0.82
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289978 c.-737T>G upstream_gene_variant 0.78
kasA 2518132 c.18C>T synonymous_variant 0.75
ahpC 2726378 c.186T>A synonymous_variant 0.78
folC 2746391 p.Val403Ala missense_variant 0.68
Rv2752c 3067009 c.-818A>G upstream_gene_variant 0.67
thyX 3067812 p.Gln45Arg missense_variant 0.79
ald 3086728 c.-92C>T upstream_gene_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.82
Rv3083 3448783 p.Val94Ile missense_variant 0.71
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475113 c.1107G>A synonymous_variant 0.68
fprA 3475159 p.Asn385Asp missense_variant 0.71
fprA 3475323 c.1317T>C synonymous_variant 0.7
Rv3236c 3612694 c.423T>C synonymous_variant 0.79
Rv3236c 3612813 p.Thr102Ala missense_variant 0.28
fbiB 3641584 p.Val17Ala missense_variant 0.72
clpC1 4039853 c.852G>A synonymous_variant 0.71
panD 4044134 p.Asp50Asn missense_variant 0.7
embC 4240671 p.Thr270Ile missense_variant 0.71
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.28
embA 4244154 p.Thr308Ala missense_variant 0.57
embA 4244220 c.988C>T synonymous_variant 0.6
embA 4244762 c.1530C>T synonymous_variant 0.69
embB 4246712 p.Val67Leu missense_variant 0.63
embB 4246864 c.351C>T synonymous_variant 0.66
embB 4247646 p.Glu378Ala missense_variant 0.74
aftB 4267647 p.Asp397Gly missense_variant 0.23
aftB 4269351 c.-515C>T upstream_gene_variant 0.75
ubiA 4269387 p.Glu149Asp missense_variant 0.74
aftB 4269606 c.-770T>C upstream_gene_variant 0.56
ethA 4327042 p.Asp144Asn missense_variant 0.67
ethA 4328211 c.-738A>G upstream_gene_variant 0.74
whiB6 4338269 p.Gly85Ser missense_variant 0.77
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.33