TB-Profiler result

Run: SRR15368707
Summary

Run ID: SRR15368707

Sample name:

Date: 03-04-2023 13:44:10

Number of reads: 5155236

Percentage reads mapped: 12.5

Strain: lineage2.2.2;lineage2.2.1

Drug-resistance: HR-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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.24
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.83
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.82 isoniazid, ethionamide
gid 4407851 c.351dupG frameshift_variant 0.89 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
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 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 764695 c.1326T>C synonymous_variant 0.1
rpoC 764706 p.Leu446Gln missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.28
mmpS5 778656 p.Ala84Thr missense_variant 0.72
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154_-153insC upstream_gene_variant 0.9
fbiC 1302782 c.-149C>G upstream_gene_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 0.21
embR 1416724 p.Trp208* stop_gained 0.68
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.14
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.17
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.18
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.17
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.17
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.17
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.18
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.23
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.18
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.18
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.23
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.22
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.15
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.12
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.11
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.11
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrl 1475108 n.1451C>G non_coding_transcript_exon_variant 0.13
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.11
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.11
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.1
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.11
rrl 1476270 n.2613G>A non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.55
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.66
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.69
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.6
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.11
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.19
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.22
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.13
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.59
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.69
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.68
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.68
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.24
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.56
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.51
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.54
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.52
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.48
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.18
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.11
rpsA 1833410 c.-132G>A upstream_gene_variant 0.17
rpsA 1833909 p.Asp123Ala missense_variant 0.69
rpsA 1834177 c.636A>C synonymous_variant 0.96
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
Rv2752c 3064631 p.Ala521Ser missense_variant 0.77
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449528 p.Ile342Thr missense_variant 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612170 p.Glu316Gly missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
ddn 3987084 p.Gly81Ser missense_variant 0.9
clpC1 4039124 c.1581C>T synonymous_variant 0.78
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.98
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 0.98