TB-Profiler result

Run: ERR4816944
Summary

Run ID: ERR4816944

Sample name:

Date: 01-04-2023 14:43:06

Number of reads: 430001

Percentage reads mapped: 80.94

Strain: lineage2.2

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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
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
rpoB 761142 p.Lys446Gln missense_variant 0.33 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.29 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.48 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 5378 p.Trp47Arg missense_variant 0.13
gyrB 5638 c.399C>T synonymous_variant 0.15
gyrA 7057 c.-245C>T upstream_gene_variant 0.17
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 1.0
mshA 575881 p.His178Gln missense_variant 0.15
rpoB 760577 p.Glu257Asp missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763699 c.330G>T synonymous_variant 0.31
rpoC 763708 c.339G>C synonymous_variant 0.27
rpoC 763714 c.345G>C synonymous_variant 0.25
rpoC 763717 c.348T>C synonymous_variant 0.25
rpoC 763718 p.Leu117Val missense_variant 0.24
rpoC 763723 c.354G>C synonymous_variant 0.25
rpoC 763724 p.Asp119Asn missense_variant 0.25
rpoC 763729 c.360G>C synonymous_variant 0.31
rpoC 763732 c.363C>G synonymous_variant 0.31
rpoC 763735 c.366G>C synonymous_variant 0.31
rpoC 763744 c.375G>C synonymous_variant 0.25
rpoC 763751 p.Ile128Val missense_variant 0.25
rpoC 763772 p.Val135Met missense_variant 0.22
rpoC 763781 p.Ser138Ala missense_variant 0.12
rpoC 764274 p.Phe302Ser missense_variant 0.15
rpoC 764605 c.1236G>C synonymous_variant 0.14
rpoC 764623 c.1254C>G synonymous_variant 0.13
rpoC 764632 c.1263T>C synonymous_variant 0.14
rpoC 764635 c.1266C>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779309 p.Arg107His missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417109 p.Arg80His missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.5
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.45
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.45
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.45
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.75
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.5
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.53
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.64
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.8
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.8
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.29
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.71
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.71
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.57
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.38
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.43
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.38
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.5
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.33
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.33
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.33
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.29
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 0.33
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.33
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.33
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.33
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.33
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.33
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.5
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.19
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.47
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.45
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.38
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.48
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.43
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.57
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.33
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.4
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.4
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.2
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.5
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.2
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.7
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.78
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.71
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.67
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.38
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.43
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.86
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.25
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.9
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.9
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.91
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.4
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.9
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.83
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.8
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.75
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.75
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.75
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.75
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.5
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 0.4
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.62
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.73
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.82
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.5
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.5
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.5
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.56
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.56
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.43
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.43
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.4
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.89
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.89
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.91
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.91
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.91
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.4
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.4
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.67
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.67
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.67
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.8
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834294 c.753G>C synonymous_variant 0.15
rpsA 1834298 p.Gln253Glu missense_variant 0.14
rpsA 1834306 c.765T>C synonymous_variant 0.17
rpsA 1834307 p.Asp256Gln missense_variant 0.17
rpsA 1834312 c.771G>A synonymous_variant 0.14
rpsA 1834327 c.786G>T synonymous_variant 0.13
rpsA 1834345 c.804C>T synonymous_variant 0.12
rpsA 1834348 c.807T>C synonymous_variant 0.12
rpsA 1834354 c.813G>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101741 c.1302G>A synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155090 p.Trp341Leu missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222263 p.Arg301Leu missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289519 c.-278T>C upstream_gene_variant 0.17
ahpC 2726226 p.Ala12Thr missense_variant 0.12
Rv2752c 3066214 c.-23G>T upstream_gene_variant 0.17
ald 3086681 c.-139T>C upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841562 c.-142A>G upstream_gene_variant 1.0
clpC1 4039592 c.1113G>A synonymous_variant 1.0
embC 4241478 p.Ala539Asp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269129 c.-293G>C upstream_gene_variant 0.18
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