TB-Profiler result

Run: ERR4821799
Summary

Run ID: ERR4821799

Sample name:

Date: 01-04-2023 17:27:34

Number of reads: 1179502

Percentage reads mapped: 94.55

Strain: lineage2.2.1

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
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 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 0.5 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 7161 p.Ala641Asp missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8182 p.Gly294Asp missense_variant 0.11
gyrA 8685 p.Ile462Val missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491348 p.Gly189Asp missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761385 p.Ala527Ser missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764458 c.1089G>C synonymous_variant 0.12
rpoC 764461 c.1092A>G synonymous_variant 0.12
rpoC 764485 c.1116G>C synonymous_variant 0.12
rpoC 764491 c.1122G>T synonymous_variant 0.12
rpoC 764503 c.1134G>T synonymous_variant 0.18
rpoC 764931 p.Ala521Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776026 p.Ser819Pro missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800977 p.Ile57Val missense_variant 0.12
fbiC 1303319 p.Asp130Gly missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416783 p.Ala189Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.62
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.25
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.33
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.56
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.2
rrs 1472133 n.288G>A non_coding_transcript_exon_variant 0.22
rrs 1472141 n.296G>A non_coding_transcript_exon_variant 0.22
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.44
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.2
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.7
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.75
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.75
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.75
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.4
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.55
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.55
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.23
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.64
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.7
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.6
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.67
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.6
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.5
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.43
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.29
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.57
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.67
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.33
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.33
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.5
rrl 1473801 n.144T>C non_coding_transcript_exon_variant 0.5
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.67
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.75
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.75
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.75
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.75
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.75
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.75
rrl 1474581 n.924C>T non_coding_transcript_exon_variant 0.8
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834183 c.642T>C synonymous_variant 0.12
rpsA 1834189 c.648G>C synonymous_variant 0.11
rpsA 1834195 c.654G>C synonymous_variant 0.1
rpsA 1834240 c.699T>C synonymous_variant 0.14
rpsA 1834246 c.705G>T synonymous_variant 0.12
rpsA 1834249 c.708T>C synonymous_variant 0.13
rpsA 1834258 c.717G>A synonymous_variant 0.12
rpsA 1834261 c.720A>G synonymous_variant 0.13
rpsA 1834264 c.723G>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103139 c.-97A>G upstream_gene_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168339 c.2274A>G synonymous_variant 0.12
PPE35 2168455 p.Val720Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290214 c.-973T>C upstream_gene_variant 0.13
folC 2747651 c.-53C>T upstream_gene_variant 0.14
thyX 3067467 p.Ala160Val missense_variant 1.0
thyX 3068145 c.-200C>A upstream_gene_variant 1.0
thyA 3073770 p.Asp234Glu missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473927 c.-79delT upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243382 c.150C>T synonymous_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244739 p.Tyr503His missense_variant 0.12
embA 4244893 p.Gly554Val missense_variant 0.13
embA 4244914 p.Leu561Pro missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267823 c.1014G>T synonymous_variant 0.11
ethR 4327030 c.-519C>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0