TB-Profiler result

Run: SRR11972450
Summary

Run ID: SRR11972450

Sample name:

Date: 03-04-2023 05:42:58

Number of reads: 1173130

Percentage reads mapped: 90.28

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 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
rpoB 761141 p.His445Gln missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155740 c.371delG frameshift_variant 0.33 isoniazid, isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.53 pyrazinamide, pyrazinamide
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
gyrB 5514 p.Gly92Val missense_variant 0.2
gyrB 5956 p.Glu239Asp missense_variant 0.22
gyrB 6179 p.Gly314Cys missense_variant 0.12
gyrB 6392 p.Gln385* stop_gained 0.18
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
mshA 576751 p.Lys468Asn missense_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620835 c.945C>G synonymous_variant 0.11
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoB 761163 p.Gly453Arg missense_variant 1.0
rpoB 761283 p.Ser493Pro missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.11
mmpL5 776021 c.2460G>C synonymous_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776717 c.1764A>G synonymous_variant 0.1
mmpL5 777157 c.1324C>A synonymous_variant 0.12
mmpL5 777164 c.1317C>T synonymous_variant 0.12
mmpL5 778516 c.-36C>T upstream_gene_variant 0.14
mmpR5 779456 p.Arg156Leu missense_variant 0.12
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 1472177 n.332C>T non_coding_transcript_exon_variant 0.25
rrs 1472194 n.349G>T non_coding_transcript_exon_variant 0.2
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.36
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.38
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.25
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.25
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.33
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.5
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.67
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.44
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.46
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.46
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.46
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.46
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.46
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.46
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.46
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.46
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.46
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.46
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.46
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.43
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.43
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.43
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.5
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.45
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.45
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.45
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.45
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.5
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.44
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.3
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.33
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.43
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.43
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.43
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.43
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.43
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.42
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.42
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.3
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.33
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.45
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.45
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.22
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.22
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.22
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.22
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.18
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.2
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
inhA 1674622 p.Gly141Arg missense_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101796 p.Ser416* stop_gained 0.15
ndh 2102035 c.1008C>G synonymous_variant 0.13
katG 2154686 p.Ala476Ser missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.17
PPE35 2167850 c.2763C>T synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168244 p.Ser790Ile missense_variant 0.13
PPE35 2169287 c.1326T>C synonymous_variant 0.21
PPE35 2169293 c.1320T>C synonymous_variant 0.22
PPE35 2169748 p.Ile289Phe missense_variant 0.11
PPE35 2169749 c.864A>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.32
PPE35 2170400 c.213G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289182 c.60G>A synonymous_variant 0.67
pncA 2289366 c.-125C>A upstream_gene_variant 1.0
kasA 2519338 c.1224T>C synonymous_variant 0.29
eis 2714941 p.Tyr131Cys missense_variant 0.12
ahpC 2726463 p.Phe91Leu missense_variant 0.17
folC 2746519 c.1080T>C synonymous_variant 0.14
folC 2747163 p.Gly146Cys missense_variant 0.2
folC 2747484 c.114delG frameshift_variant 0.15
thyA 3073694 p.Pro260Thr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087311 c.492C>T synonymous_variant 0.14
ald 3087342 p.Gly175Ser missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568426 p.Arg85Leu missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878109 p.Lys133Asn missense_variant 0.12
clpC1 4039017 p.Ser563Tyr missense_variant 0.13
clpC1 4039320 p.Ala462Val missense_variant 0.15
clpC1 4039419 p.Ala429Asp missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243051 p.Leu1063Phe missense_variant 0.12
embA 4243190 c.-43G>C upstream_gene_variant 0.88
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244857 c.1629delG frameshift_variant 0.18
embA 4245728 p.Leu832Phe missense_variant 1.0
embA 4246273 p.Thr1014Met missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.31
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267968 p.Leu290Pro missense_variant 0.17
aftB 4268578 p.Ala87Thr missense_variant 0.12
ethR 4326639 c.-910G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407796 p.Ser136Leu missense_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408066 p.Asp46Val missense_variant 0.22