TB-Profiler result

Run: ERR1873557

Summary

Run ID: ERR1873557

Sample name:

Date: 15-08-2022 11:08:13

Number of reads: 2167080

Percentage reads mapped: 47.36

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB


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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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.78 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 1.0 ethionamide
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 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762286 p.Arg827His missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T 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
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.3
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.27
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.27
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.25
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.23
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.23
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.23
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.23
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.14
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.22
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.27
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.27
rrs 1472350 n.505C>T non_coding_transcript_exon_variant 0.27
rrs 1472373 n.528G>A non_coding_transcript_exon_variant 0.33
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.33
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.33
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.35
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.35
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.35
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.28
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.28
rrs 1472694 n.849C>G non_coding_transcript_exon_variant 0.1
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.16
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.39
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.38
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.39
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.58
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.57
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.57
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.53
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.42
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.25
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.26
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.38
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.39
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.38
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.38
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.38
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.4
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.37
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.33
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.31
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.29
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.33
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.33
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.34
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.34
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.36
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.37
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.37
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.38
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.35
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.32
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.34
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.29
rrs 1473097 n.1252G>C non_coding_transcript_exon_variant 0.28
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.28
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.25
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.27
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.42
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.41
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.4
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.4
rrs 1473193 n.1348G>A non_coding_transcript_exon_variant 0.39
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.39
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.4
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.39
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.4
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.39
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.46
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.46
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.45
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.47
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.49
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.49
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.48
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.68
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.65
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.68
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.71
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.62
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.62
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.58
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.58
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.55
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.56
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.34
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.26
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.28
thyA 3073806 c.666C>G synonymous_variant 0.14
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
embC 4242425 p.Arg855Gly missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.25
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
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
pncA 2288686 c.-327_555del start_lost&conservative_inframe_deletion 1.0