TB-Profiler result

Run: SRR14782555
Summary

Run ID: SRR14782555

Sample name:

Date: 03-04-2023 11:30:24

Number of reads: 622862

Percentage reads mapped: 25.35

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 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.96
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288778 p.Val155Gly missense_variant 0.9 pyrazinamide
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 4247431 p.Met306Ile 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 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575156 c.-192G>A upstream_gene_variant 0.25
mshA 575248 c.-100C>A upstream_gene_variant 0.13
mshA 575460 p.Val38Ala missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576446 p.Thr367Pro missense_variant 0.33
mshA 576496 p.Asp383Glu missense_variant 0.22
mshA 576616 c.1269G>C synonymous_variant 0.6
ccsA 620625 p.Ile245Met missense_variant 0.79
rpoB 761268 p.Ile488Val missense_variant 0.92
rpoB 761470 p.Val555Gly missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_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
mmpL5 777883 p.Gly200Arg missense_variant 0.27
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 0.91
embR 1416435 p.Ala305Pro missense_variant 0.23
atpE 1461235 p.Tyr64Phe missense_variant 0.12
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 0.18
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.3
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.3
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 0.3
rrs 1472135 n.290C>G non_coding_transcript_exon_variant 0.3
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.3
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.32
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.32
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.32
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.3
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.5
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.44
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.22
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.13
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.12
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.15
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.15
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.2
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.2
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.53
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.53
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.52
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.54
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.52
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.17
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.11
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.21
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.21
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.23
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.22
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.26
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.16
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.19
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 0.24
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.19
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.2
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.28
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.28
rrl 1475870 n.2213G>A non_coding_transcript_exon_variant 0.26
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.18
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.61
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.64
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.79
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.78
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.81
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.84
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.84
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.84
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.82
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.84
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.84
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.85
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.87
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.87
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.89
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.89
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.89
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.88
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.68
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.29
fabG1 1673553 p.Asp38Glu missense_variant 0.62
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102535 c.508C>T synonymous_variant 0.11
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 2289709 c.-468G>T upstream_gene_variant 0.18
folC 2747459 p.Leu47Pro missense_variant 0.2
pepQ 2859918 c.501A>C synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 1.0
Rv3236c 3612537 p.Gly194Trp missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 0.9
fbiB 3641810 c.276G>C synonymous_variant 1.0
clpC1 4040244 p.Gly154Ala missense_variant 0.2
embC 4240409 p.Pro183Ala missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247016 p.Ser168Trp missense_variant 0.25
embB 4247020 c.507C>G synonymous_variant 0.6
embB 4248189 p.Arg559Gln missense_variant 0.14
embB 4248324 p.Ala604Gly missense_variant 0.25
embB 4248328 c.1815G>C synonymous_variant 0.38
aftB 4267647 p.Asp397Gly missense_variant 0.93
aftB 4267649 c.1188T>G synonymous_variant 0.21
ethA 4326339 p.Asn379Asp 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 0.93
gid 4408093 p.Gly37Ala missense_variant 0.25