TB-Profiler result

Run: SRR7645853
Summary

Run ID: SRR7645853

Sample name:

Date: 04-04-2023 19:55:21

Number of reads: 6481895

Percentage reads mapped: 64.25

Strain: lineage2.2.1

Drug-resistance: MDR-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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 1.0 para-aminosalicylic_acid
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
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 0.98
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764916 p.Leu516Pro missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_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 779615 c.-710C>G upstream_gene_variant 1.0
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 1472106 n.261G>A non_coding_transcript_exon_variant 0.18
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.2
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.22
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.22
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 0.22
rrs 1472135 n.290C>G non_coding_transcript_exon_variant 0.23
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.22
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.23
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.24
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.24
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.29
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.13
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.14
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.44
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.44
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.43
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.45
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.42
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.13
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.18
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.24
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.25
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.26
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.25
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.26
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.26
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.35
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.35
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.45
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.46
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.47
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.47
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 0.47
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.47
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.47
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.55
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.58
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.59
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.49
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.48
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.46
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.45
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.44
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.24
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.14
rrl 1476588 n.2931A>G non_coding_transcript_exon_variant 0.14
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.14
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.13
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.13
rrl 1476611 n.2954T>C non_coding_transcript_exon_variant 0.13
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.13
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.13
rrl 1476621 n.2964C>T non_coding_transcript_exon_variant 0.13
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.13
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.13
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.13
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
pncA 2289120 p.Tyr41Cys missense_variant 0.99
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
fbiB 3641810 c.276G>C synonymous_variant 1.0
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
ethA 4326339 p.Asn379Asp missense_variant 0.99
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