TB-Profiler result

Run: SRR3732700
Summary

Run ID: SRR3732700

Sample name:

Date: 04-04-2023 05:38:02

Number of reads: 826472

Percentage reads mapped: 99.57

Strain: lineage2.2

Drug-resistance: Other

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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
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
ethA 4327348 c.125delG frameshift_variant 0.25 ethionamide, ethionamide
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 5107 c.-133C>A upstream_gene_variant 0.12
gyrB 5407 c.168G>A synonymous_variant 0.25
gyrB 5425 c.186A>G synonymous_variant 0.25
gyrB 6283 p.Asp348Glu missense_variant 0.33
gyrB 6562 p.Lys441Asn missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7699 p.Arg133Gln missense_variant 0.4
gyrA 8721 c.1420C>A synonymous_variant 0.5
gyrA 9304 p.Gly668Asp missense_variant 0.9
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620523 c.633G>T synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760433 p.Asp209Glu missense_variant 0.25
rpoB 762120 p.Asp772Asn missense_variant 0.29
rpoB 762681 p.Glu959Lys missense_variant 0.33
rpoB 762697 p.Ala964Asp missense_variant 0.4
rpoB 762712 p.Pro969Gln missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764652 p.Ser428Leu missense_variant 0.4
rpoC 764987 p.Gln540Lys missense_variant 0.25
rpoC 765960 p.Ala864Glu missense_variant 0.15
rpoC 765992 c.2623C>A synonymous_variant 0.17
rpoC 766096 c.2727G>T synonymous_variant 0.25
rpoC 766849 p.Gln1160His missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775840 p.Val881Leu missense_variant 0.67
mmpL5 776051 p.Leu810Phe missense_variant 0.4
mmpL5 776066 c.2415C>T synonymous_variant 0.33
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777200 c.1281C>T synonymous_variant 0.33
mmpL5 777747 p.Gly245Val missense_variant 0.4
mmpL5 777937 p.Val182Ile missense_variant 0.29
mmpL5 778008 p.Gly158Val missense_variant 0.18
mmpL5 778416 p.Pro22Leu missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779630 c.-725T>C upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>T upstream_gene_variant 0.33
rpsL 781491 c.-69C>A upstream_gene_variant 0.4
rpsL 781737 p.Gln60Lys missense_variant 0.25
rplC 801221 p.Ser138Ile missense_variant 0.22
fbiC 1303268 p.Lys113Met missense_variant 0.33
fbiC 1303328 p.Arg133His missense_variant 0.33
fbiC 1303913 p.Gly328Val missense_variant 0.2
fbiC 1304552 p.Gly541Val missense_variant 0.25
Rv1258c 1406522 c.819G>T synonymous_variant 0.4
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417120 c.228G>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673276 c.-164G>A upstream_gene_variant 0.33
inhA 1674929 p.Cys243Ser missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834219 c.678C>T synonymous_variant 0.29
rpsA 1834621 p.Leu360Phe missense_variant 0.25
rpsA 1834725 c.1185delC frameshift_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101931 p.Ala371Asp missense_variant 0.29
katG 2154523 p.Ser530Tyr missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154941 p.Glu391* stop_gained 0.25
katG 2155229 p.Gln295Lys missense_variant 0.67
katG 2155781 p.Gly111Ser missense_variant 0.22
katG 2155813 p.Pro100Leu missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289445 c.-204C>A upstream_gene_variant 0.25
pncA 2289707 c.-466A>T upstream_gene_variant 0.29
pncA 2289772 c.-531C>A upstream_gene_variant 0.29
kasA 2518561 c.447T>G synonymous_variant 0.17
eis 2714813 p.Glu174* stop_gained 0.25
ahpC 2726246 c.54C>A synonymous_variant 0.33
folC 2747248 c.351G>T synonymous_variant 0.17
pepQ 2859964 p.Ala152Val missense_variant 0.22
Rv2752c 3065040 c.1152C>A synonymous_variant 0.14
Rv2752c 3065116 p.Gly359Val missense_variant 0.22
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.95
thyX 3067661 c.285C>A synonymous_variant 0.2
thyX 3068037 c.-92C>A upstream_gene_variant 0.22
thyX 3068128 c.-183C>T upstream_gene_variant 0.25
thyA 3073767 c.705G>T synonymous_variant 0.5
thyA 3073988 p.Gln162Lys missense_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087755 c.936G>T synonymous_variant 1.0
Rv3083 3448560 c.57G>A synonymous_variant 0.2
Rv3083 3448924 p.Gly141Ser missense_variant 0.67
Rv3083 3449310 c.807G>T synonymous_variant 0.33
fprA 3473895 c.-112T>A upstream_gene_variant 0.22
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3474319 p.Gly105Ser missense_variant 0.22
fprA 3474825 c.819C>G synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640794 c.-741A>G upstream_gene_variant 0.2
fbiA 3641158 p.Ala206Ser missense_variant 0.25
fbiB 3642072 p.Arg180Cys missense_variant 0.13
fbiB 3642729 p.Gly399Cys missense_variant 0.33
alr 3840548 c.872delA frameshift_variant 0.12
alr 3840613 p.Gly270Trp missense_variant 0.12
rpoA 3877801 p.Pro236Gln missense_variant 0.33
rpoA 3877920 c.588G>T synonymous_variant 0.5
ddn 3987083 c.240C>A synonymous_variant 0.67
clpC1 4038578 p.Phe709Leu missense_variant 0.29
clpC1 4038943 c.1762C>A synonymous_variant 0.4
clpC1 4040778 c.-74G>A upstream_gene_variant 0.29
embC 4239950 c.88C>A synonymous_variant 0.29
embC 4241658 p.Ser599* stop_gained 1.0
embC 4241773 c.1911C>A synonymous_variant 0.5
embC 4242066 p.Ser735* stop_gained 0.2
embC 4242090 p.Ala743Asp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243275 p.Leu15Ile missense_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245183 p.Leu651Met missense_variant 0.25
embA 4245512 c.2280G>T synonymous_variant 0.5
embA 4246204 p.Arg991Leu missense_variant 0.33
embB 4246936 c.423G>T synonymous_variant 0.15
embB 4246978 c.465C>T synonymous_variant 0.14
embB 4247225 p.Arg238Ser missense_variant 0.18
embB 4247427 p.Gly305Asp missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268435 c.402C>T synonymous_variant 0.33
ubiA 4269736 p.Leu33Gln missense_variant 0.22
ethA 4326078 c.1396C>A synonymous_variant 0.67
ethA 4326692 p.Arg261Leu missense_variant 0.13
ethR 4327597 p.Thr17Ser missense_variant 0.67
whiB6 4338487 p.Cys12Phe missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407726 p.Met159Ile missense_variant 0.25
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408031 p.Leu58Ile missense_variant 0.29
gid 4408281 c.-79C>A upstream_gene_variant 0.5