TB-Profiler result

Run: SRR3732708
Summary

Run ID: SRR3732708

Sample name:

Date: 04-04-2023 05:38:27

Number of reads: 1252207

Percentage reads mapped: 99.61

Strain: lineage2.2.1.1

Drug-resistance: Sensitive

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
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 5434 c.195G>T synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7894 p.Ala198Val missense_variant 0.33
gyrA 8650 p.Arg450His missense_variant 0.2
gyrA 9111 p.Pro604Thr missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9628 p.Ala776Asp missense_variant 0.17
fgd1 491018 p.Phe79Ser missense_variant 0.22
fgd1 491447 p.Val222Ala missense_variant 0.25
fgd1 491728 p.Asp316Tyr missense_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576273 p.Pro309Leu missense_variant 0.13
ccsA 620526 c.636G>T synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760771 p.Ile322Thr missense_variant 0.11
rpoB 762059 c.2253C>T synonymous_variant 0.17
rpoB 762555 p.Pro917Ser missense_variant 0.15
rpoB 762584 p.Leu926Phe missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764363 p.Gly332Cys missense_variant 0.33
rpoC 764875 c.1506C>A synonymous_variant 0.22
rpoC 764890 p.Leu507Phe missense_variant 0.22
rpoC 764959 p.Glu530Asp missense_variant 0.12
rpoC 765366 p.Thr666Asn missense_variant 0.12
rpoC 765755 p.Asp796Tyr missense_variant 0.22
rpoC 766426 c.3057C>A synonymous_variant 0.14
rpoC 766891 c.3527delT frameshift_variant 0.13
rpoC 767001 p.Thr1211Met missense_variant 0.33
rpoC 767066 p.Leu1233Met missense_variant 0.18
rpoC 767285 p.Pro1306Thr missense_variant 0.18
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 776195 c.2286G>A synonymous_variant 0.29
mmpL5 777203 c.1278G>T synonymous_variant 0.4
mmpL5 778000 p.Leu161Met missense_variant 0.12
mmpL5 779157 c.-677C>A upstream_gene_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781647 p.Arg30Ser missense_variant 0.67
fbiC 1303299 p.Met123Ile missense_variant 0.18
Rv1258c 1406712 p.Ser210Tyr missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416367 p.Arg327Gln missense_variant 0.17
embR 1417380 c.-33C>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472549 n.704G>T non_coding_transcript_exon_variant 0.25
rrl 1475278 n.1621G>T non_coding_transcript_exon_variant 0.33
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.67
fabG1 1673760 p.Lys107Asn missense_variant 0.2
inhA 1674428 p.Gly76Val missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834526 p.Arg329Ser missense_variant 0.17
rpsA 1834790 c.1249C>A synonymous_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102756 p.Gly96Glu missense_variant 0.5
katG 2154629 p.Gly495Ser missense_variant 0.5
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169375 p.Asn413Ile missense_variant 0.18
PPE35 2169422 c.1191G>T synonymous_variant 0.22
PPE35 2170028 p.Met195Ile missense_variant 0.2
Rv1979c 2223123 c.42G>T synonymous_variant 0.5
Rv1979c 2223161 p.Val2Leu missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288901 p.Thr114Lys missense_variant 0.17
pncA 2290134 c.-893G>A upstream_gene_variant 0.4
kasA 2518805 p.Asp231Asn missense_variant 0.14
kasA 2519324 p.Phe404Leu missense_variant 0.25
eis 2714308 p.Pro342Gln missense_variant 0.29
eis 2714456 p.Gly293Ser missense_variant 0.13
eis 2714655 p.Tyr226* stop_gained 0.25
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2715163 p.Glu57Gly missense_variant 1.0
eis 2715248 p.Gly29Cys missense_variant 0.2
eis 2715356 c.-24C>T upstream_gene_variant 0.17
folC 2747025 p.Ala192Thr missense_variant 0.22
pepQ 2859464 p.Gly319Ser missense_variant 0.2
pepQ 2860547 c.-129C>A upstream_gene_variant 0.14
Rv2752c 3065102 p.Thr364Ser missense_variant 0.22
Rv2752c 3065584 p.Ser203* stop_gained 0.17
thyX 3067921 p.Val9Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474133 p.Pro43Thr missense_variant 0.13
fprA 3475207 p.Asp401Tyr missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641074 p.Ala178Thr missense_variant 0.17
fbiB 3642867 p.Leu445Met missense_variant 0.12
alr 3840629 c.792C>T synonymous_variant 0.18
alr 3840790 p.Gln211Lys missense_variant 0.18
alr 3841518 c.-98C>A upstream_gene_variant 0.2
rpoA 3877838 p.Glu224* stop_gained 0.18
rpoA 3878163 c.345C>A synonymous_variant 0.15
clpC1 4038773 p.Asp644Glu missense_variant 0.12
clpC1 4038776 p.Glu643Asp missense_variant 0.12
clpC1 4038782 c.1923G>C synonymous_variant 0.12
clpC1 4038938 p.Phe589Leu missense_variant 0.29
clpC1 4039733 c.972G>T synonymous_variant 0.22
clpC1 4040308 c.397C>A synonymous_variant 0.17
clpC1 4040851 c.-147T>A upstream_gene_variant 0.29
embC 4242122 p.Asp754Tyr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242838 c.-395C>T upstream_gene_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243676 c.444G>T synonymous_variant 0.12
embA 4245349 p.Ala706Val missense_variant 0.29
embA 4246068 p.Pro946Thr missense_variant 0.5
embB 4246615 c.102G>A synonymous_variant 0.12
embB 4247093 p.Gly194Trp missense_variant 0.13
embB 4247489 p.Pro326Ser missense_variant 0.25
embB 4247930 p.Val473Ile missense_variant 0.12
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248692 p.Val727Leu missense_variant 0.29
aftB 4267522 p.Leu439Ile missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4270025 c.-192C>A upstream_gene_variant 0.12
ethA 4326651 p.Gly275Trp missense_variant 0.15
ethA 4327041 p.Glu145* stop_gained 0.4
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
gid 4407977 p.Gly76Ser missense_variant 0.14