TB-Profiler result

Run: ERR1750934

Summary

Run ID: ERR1750934

Sample name:

Date: 31-03-2023 15:00:44

Number of reads: 1005414

Percentage reads mapped: 95.75

Strain: lineage2.2.1

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 5152 c.-88C>T upstream_gene_variant 0.22
gyrB 5212 c.-28C>T upstream_gene_variant 0.2
gyrB 5409 p.Ala57Val missense_variant 0.25
gyrB 6199 p.Phe320Leu missense_variant 0.22
gyrB 7030 c.1794delG frameshift_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7525 p.Arg75Leu missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7974 p.Gly225Cys missense_variant 0.33
gyrA 8882 c.1581G>A synonymous_variant 0.4
gyrA 9147 p.Gly616Ser missense_variant 0.29
gyrA 9162 p.Pro621Ser missense_variant 0.2
gyrA 9272 p.Asp657Glu missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9565 p.Tyr755Phe missense_variant 0.17
gyrA 9661 p.Ala787Val missense_variant 0.18
fgd1 491014 p.Thr78Pro missense_variant 0.38
fgd1 491328 c.546C>G synonymous_variant 1.0
fgd1 491330 p.Lys183Met missense_variant 1.0
fgd1 491651 p.Pro290His missense_variant 0.5
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576750 p.Lys468Thr missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.4
rpoB 761005 p.Thr400Ile missense_variant 0.5
rpoB 761016 p.Glu404* stop_gained 0.4
rpoB 762148 p.Arg781Leu missense_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763542 p.Trp58* stop_gained 0.5
rpoC 764333 p.Pro322Ser missense_variant 0.4
rpoC 764893 c.1524T>A synonymous_variant 0.5
mmpL5 775592 c.2889G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776344 p.Gly713Trp missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800820 p.Lys4Asn missense_variant 0.4
rplC 801025 p.Ala73Thr missense_variant 0.22
rplC 801272 p.Ala155Gly missense_variant 0.33
fbiC 1303121 p.Arg64Leu missense_variant 0.13
fbiC 1303290 p.Ser120Arg missense_variant 0.29
fbiC 1304953 p.Glu675* stop_gained 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416271 c.1077C>T synonymous_variant 0.33
embR 1417173 p.Leu59Phe missense_variant 0.29
embR 1417181 p.Ile56Asn missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474682 n.1025A>T non_coding_transcript_exon_variant 0.2
rrl 1474683 n.1026C>T non_coding_transcript_exon_variant 0.2
rrl 1475029 n.1372T>C non_coding_transcript_exon_variant 1.0
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.15
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.22
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.22
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.29
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.29
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.38
rrl 1476236 n.2579G>T non_coding_transcript_exon_variant 0.22
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.38
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.38
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.38
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.43
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.33
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.33
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.33
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.33
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.33
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.33
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.33
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.33
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.33
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.33
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.5
rrl 1476631 n.2974G>T non_coding_transcript_exon_variant 0.5
fabG1 1673298 c.-142A>T upstream_gene_variant 0.29
fabG1 1673347 c.-93C>A upstream_gene_variant 0.33
fabG1 1673417 c.-23C>A upstream_gene_variant 0.29
inhA 1674802 p.Ala201Ser missense_variant 0.18
rpsA 1834665 p.Pro375Gln missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.31
katG 2154612 c.1500G>A synonymous_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222493 c.672C>A synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288904 p.Gly113Asp missense_variant 0.33
kasA 2519330 p.Gly406Ser missense_variant 0.18
eis 2714566 p.Leu256Pro missense_variant 0.67
eis 2714891 p.Arg148Cys missense_variant 0.2
eis 2714955 p.Tyr126* stop_gained 0.15
folC 2746505 p.Thr365Met missense_variant 0.17
pepQ 2859333 p.Leu362Phe missense_variant 0.5
ribD 2986992 p.Gly52Cys missense_variant 0.33
Rv2752c 3066195 c.-5delC upstream_gene_variant 0.33
thyA 3073886 p.Val196Phe missense_variant 0.33
ald 3086622 c.-198C>T upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086982 p.Ala55Thr missense_variant 0.33
ald 3087335 c.516G>A synonymous_variant 0.2
fbiD 3338949 c.-169G>T upstream_gene_variant 0.5
fbiD 3339402 c.285C>T synonymous_variant 0.18
Rv3083 3449324 p.Arg274Leu missense_variant 0.33
Rv3083 3449396 p.Cys298Tyr missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474051 c.45G>T synonymous_variant 0.22
fprA 3474814 p.Arg270Trp missense_variant 0.22
fprA 3474914 p.Ala303Val missense_variant 0.14
fprA 3475233 p.Trp409Cys missense_variant 0.18
fprA 3475288 p.Ala428Thr missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642844 c.1313delC frameshift_variant 0.18
alr 3840550 p.Glu291Lys missense_variant 0.17
rpoA 3878096 p.Leu138Phe missense_variant 0.5
clpC1 4039365 p.Ala447Asp missense_variant 0.25
clpC1 4040756 c.-52T>A upstream_gene_variant 0.29
clpC1 4040791 c.-90_-88delGGA upstream_gene_variant 0.22
embC 4241785 p.Trp641* stop_gained 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243128 p.Ala1089Val missense_variant 0.25
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246422 p.Val1064Met missense_variant 0.18
aftB 4267003 p.Arg612Trp missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267970 c.867C>T synonymous_variant 0.25
aftB 4268006 c.831A>T synonymous_variant 0.25
aftB 4268831 c.6C>A synonymous_variant 0.13
ubiA 4269121 p.Phe238Tyr missense_variant 0.33
ubiA 4269140 p.Cys232Ser missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407720 c.483C>A synonymous_variant 0.22
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408341 c.-139G>A upstream_gene_variant 0.25