TB-Profiler result

Run: SRR7755705
Summary

Run ID: SRR7755705

Sample name:

Date: 04-04-2023 20:15:56

Number of reads: 3567219

Percentage reads mapped: 76.49

Strain: lineage4.2.1;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 0.25
lineage4 Euro-American LAM;T;S;X;H None 0.73
lineage4.2 Euro-American H;T;LAM None 0.75
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.23
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.25
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.77
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 0.26 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.64 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.75 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288764 p.Thr160Ala missense_variant 0.21 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.76 kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 0.25 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 0.48 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.77 ethambutol
embB 4247402 p.Ser297Ala missense_variant 0.67 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.25 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.3 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 1.0
fgd1 491247 c.465C>T synonymous_variant 0.78
fgd1 491742 c.960T>C synonymous_variant 0.18
mshA 575907 p.Ala187Val missense_variant 0.2
ccsA 619969 p.Val27Ile missense_variant 0.67
ccsA 620625 p.Ile245Met missense_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 0.24
rpoC 764817 p.Val483Gly missense_variant 0.75
rpoC 766645 p.Glu1092Asp missense_variant 0.26
rpoC 766779 p.Glu1137Gly missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.45
mmpL5 776182 p.Asp767Asn missense_variant 0.26
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.19
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.22
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.23
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.24
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 0.24
rrs 1472135 n.290C>G non_coding_transcript_exon_variant 0.24
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.22
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.22
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.23
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.23
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.24
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.26
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.12
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.12
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.23
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.23
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.47
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.45
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.42
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.41
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.38
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.12
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.12
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.2
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.22
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.23
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.22
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.23
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.22
rrl 1476091 n.2434T>C non_coding_transcript_exon_variant 0.37
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.11
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.11
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.2
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.2
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.24
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.25
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.25
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.26
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.39
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.45
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.45
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.43
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.41
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.4
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.37
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.24
rpsA 1834177 c.636A>C synonymous_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 0.29
PPE35 2169879 p.Phe245Cys missense_variant 0.61
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.72
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 0.35
fbiB 3641810 c.276G>C synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 0.97
embA 4243460 c.228C>T synonymous_variant 0.21
embB 4249594 c.3081G>A synonymous_variant 0.67
aftB 4267647 p.Asp397Gly missense_variant 0.16
ethA 4326339 p.Asn379Asp missense_variant 0.28
ethA 4326632 p.His281Pro missense_variant 0.77
ethA 4328376 c.-903G>C upstream_gene_variant 0.66
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 0.22