TB-Profiler result

Run: ERR1750916
Summary

Run ID: ERR1750916

Sample name:

Date: 31-03-2023 14:59:33

Number of reads: 1909707

Percentage reads mapped: 89.29

Strain: lineage2.2.1.1

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
lineage2 East-Asian Beijing RD105 0.94
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.96
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.96
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.17 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.18 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
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 491742 c.960T>C synonymous_variant 0.96
mshA 575907 p.Ala187Val missense_variant 0.93
ccsA 620625 p.Ile245Met missense_variant 0.94
rpoB 760871 c.1065C>G synonymous_variant 0.14
rpoB 762942 p.Ile1046Val missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.9
rpoC 764569 p.Lys400Asn missense_variant 0.13
rpoC 764716 c.1347G>C synonymous_variant 0.12
rpoC 764752 c.1383G>C synonymous_variant 0.12
rpoC 765381 p.Val671Ala missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.88
mmpL5 777009 p.Pro491Arg missense_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302882 c.-49C>T upstream_gene_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472132 n.287A>G non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.19
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472188 n.343A>G non_coding_transcript_exon_variant 0.15
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 0.22
rrs 1473269 n.1424C>T non_coding_transcript_exon_variant 0.17
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.17
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.13
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.21
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.19
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.3
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.3
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.33
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.33
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.29
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.43
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.22
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.25
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.17
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.12
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.12
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.13
rrl 1475867 n.2210G>A non_coding_transcript_exon_variant 0.15
rrl 1475880 n.2223C>A non_coding_transcript_exon_variant 0.18
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.27
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.2
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.2
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.2
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.2
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.18
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.22
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.29
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.15
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.13
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.19
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.13
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.15
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.15
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.26
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
rpsA 1833736 c.195C>G synonymous_variant 0.14
rpsA 1833742 c.201A>G synonymous_variant 0.14
rpsA 1833745 c.204G>C synonymous_variant 0.14
rpsA 1833769 c.228C>G synonymous_variant 0.18
rpsA 1833781 c.240T>C synonymous_variant 0.21
rpsA 1833782 p.Ser81Lys missense_variant 0.21
rpsA 1833790 c.249T>C synonymous_variant 0.2
rpsA 1833808 c.267G>C synonymous_variant 0.14
rpsA 1833811 c.270G>C synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102596 c.447C>G synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.84
PPE35 2167926 p.Leu896Ser missense_variant 0.89
Rv1979c 2223014 p.Tyr51Asn missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288901 p.Thr114Met missense_variant 1.0
pncA 2290049 c.-808C>T upstream_gene_variant 0.17
eis 2714846 p.Val163Ile missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449105 p.Pro201His missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568455 c.225G>A synonymous_variant 0.2
Rv3236c 3612354 p.Thr255Ser missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 0.9
rpoA 3877532 p.Ala326Thr missense_variant 0.17
rpoA 3877555 p.Ser318Leu missense_variant 0.17
clpC1 4038842 c.1863G>C synonymous_variant 0.13
clpC1 4038959 p.Met582Ile missense_variant 0.2
clpC1 4039169 p.Glu512Asp missense_variant 0.12
clpC1 4039172 c.1533A>G synonymous_variant 0.11
clpC1 4039183 c.1522T>C synonymous_variant 0.11
clpC1 4039328 c.1377A>G synonymous_variant 0.14
clpC1 4039909 p.Glu266Gln missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248919 c.2406C>T synonymous_variant 0.14
aftB 4267261 p.Ile526Phe missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.84
aftB 4268421 p.Leu139Arg missense_variant 0.12
aftB 4269531 c.-695G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407927 p.Glu92Asp missense_variant 0.93