TB-Profiler result

Run: SRR11972232
Summary

Run ID: SRR11972232

Sample name:

Date: 03-04-2023 05:32:50

Number of reads: 222556

Percentage reads mapped: 99.5

Strain: lineage2.2.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
katG 2155187 p.Gly309Ser missense_variant 0.14 isoniazid
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 5363 p.Leu42Ile missense_variant 0.18
gyrB 5423 p.Ala62Ser missense_variant 0.2
gyrB 5528 p.Asp97Asn missense_variant 0.25
gyrB 5896 c.657C>T synonymous_variant 0.22
gyrB 6181 c.942C>T synonymous_variant 0.4
gyrB 6214 c.975G>A synonymous_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8108 c.807G>A synonymous_variant 0.17
gyrA 8607 c.1306C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9388 p.Ala696Val missense_variant 0.25
gyrA 9563 p.Met754Ile missense_variant 0.25
gyrA 9757 p.Ala819Val missense_variant 0.22
fgd1 490593 c.-190G>A upstream_gene_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576266 p.Ala307Thr missense_variant 0.33
ccsA 619747 c.-144C>T upstream_gene_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759671 c.-136G>A upstream_gene_variant 0.2
rpoB 760537 p.Glu244Val missense_variant 0.29
rpoB 760938 c.1132C>T synonymous_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767286 p.Pro1306Leu missense_variant 0.29
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 776516 p.Met655Ile missense_variant 0.17
mmpL5 778228 p.Gly85Arg missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302768 c.-163G>C upstream_gene_variant 0.17
fbiC 1304905 p.Ala659Pro missense_variant 0.12
fbiC 1305332 p.Glu801Gly missense_variant 0.18
fbiC 1305439 p.Ala837Thr missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416230 p.Asp373Val missense_variant 0.18
embR 1416792 p.Arg186Trp missense_variant 0.25
embR 1416848 p.Val167Glu missense_variant 0.5
embR 1417256 p.Gly31Asp missense_variant 0.15
atpE 1461207 p.Ile55Phe missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473522 n.-136T>C upstream_gene_variant 0.15
rrl 1475129 n.1472G>T non_coding_transcript_exon_variant 0.2
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.18
rrl 1476095 n.2438C>A non_coding_transcript_exon_variant 0.17
fabG1 1673734 p.Arg99Trp missense_variant 0.17
rpsA 1833473 c.-69C>T upstream_gene_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834857 p.Glu439Gly missense_variant 0.25
rpsA 1834983 p.Ala481Val missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102015 p.Val343Asp missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156280 c.-169T>C upstream_gene_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221745 p.Val474Phe missense_variant 0.18
Rv1979c 2221945 p.Val407Glu missense_variant 0.12
Rv1979c 2222014 p.Val384Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518984 c.870G>A synonymous_variant 0.17
eis 2714371 p.Leu321His missense_variant 0.12
eis 2714846 p.Val163Ile missense_variant 1.0
folC 2746415 p.Glu395Val missense_variant 0.2
Rv2752c 3065164 p.Gly343Asp missense_variant 0.25
Rv2752c 3066256 c.-65C>T upstream_gene_variant 0.18
Rv2752c 3067053 c.-862C>T upstream_gene_variant 0.12
thyX 3067682 c.264G>A synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338994 c.-124G>A upstream_gene_variant 0.17
Rv3083 3448759 p.Ala86Thr missense_variant 0.33
Rv3083 3449541 c.1038C>T synonymous_variant 0.2
Rv3083 3449953 p.His484Asp missense_variant 0.2
fprA 3473899 c.-108C>G upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612832 c.285C>T synonymous_variant 0.2
fbiA 3640606 p.Leu22Met missense_variant 0.29
fbiB 3642320 c.786C>A synonymous_variant 0.5
alr 3840231 p.Arg397His missense_variant 0.15
alr 3840676 p.Asp249Tyr missense_variant 0.13
alr 3841098 p.Pro108Leu missense_variant 0.17
rpoA 3878641 c.-135delG upstream_gene_variant 0.33
clpC1 4038186 p.Ala840Val missense_variant 0.33
clpC1 4038650 c.2055C>T synonymous_variant 0.2
clpC1 4039042 p.Ser555Thr missense_variant 0.14
panD 4044374 c.-93G>A upstream_gene_variant 0.4
embC 4240970 p.Ala370Thr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243953 p.Arg241Cys missense_variant 0.11
embA 4246372 p.Arg1047His missense_variant 1.0
embB 4246694 p.Arg61Trp missense_variant 0.22
embB 4247915 p.Arg468Cys missense_variant 0.22
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248399 p.Leu629Gln missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326361 c.1113C>A synonymous_variant 0.17
ethA 4326915 p.Ala187Thr missense_variant 0.25
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