TB-Profiler result

Run: ERR4831717
Summary

Run ID: ERR4831717

Sample name:

Date: 01-04-2023 21:04:46

Number of reads: 534252

Percentage reads mapped: 96.24

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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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 0.92 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288979 p.Ser88* stop_gained 0.15 pyrazinamide
embB 4247429 p.Met306Val 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 7344 p.Ile15Val missense_variant 0.1
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 490601 c.-182G>A upstream_gene_variant 0.29
fgd1 491436 c.654T>C synonymous_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575717 p.Asp124Asn missense_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620116 p.Val76Phe missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759818 c.12C>A synonymous_variant 0.14
rpoB 760064 p.Glu86Asp missense_variant 0.17
rpoB 761415 p.Gln537* stop_gained 0.25
rpoB 761908 p.Cys701Tyr missense_variant 0.22
rpoB 761970 p.Gly722Cys missense_variant 0.17
rpoB 762630 p.Ala942Thr missense_variant 0.13
rpoC 762794 c.-576C>A upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763921 c.552G>T synonymous_variant 0.5
rpoC 764060 p.Pro231Thr missense_variant 0.18
rpoC 764386 p.Asp339Glu missense_variant 0.11
rpoC 764902 c.1533C>A synonymous_variant 0.17
rpoC 765703 c.2336delA frameshift_variant 0.25
rpoC 766267 c.2899_2902delACGT frameshift_variant 0.18
rpoC 766275 p.Ala969Gly missense_variant 0.17
rpoC 766278 c.2909_2910insACGT frameshift_variant 0.17
rpoC 767007 p.Ala1213Glu 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 777350 c.1131G>T synonymous_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 0.87
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.4
fbiC 1304343 c.1413T>G synonymous_variant 1.0
fbiC 1304487 c.1557C>A synonymous_variant 0.22
fbiC 1304643 p.Lys571Asn missense_variant 0.12
fbiC 1304695 c.1768delG frameshift_variant 0.15
fbiC 1305103 p.Val725Leu missense_variant 0.17
fbiC 1305264 c.2334C>T synonymous_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406862 p.Ile160Thr missense_variant 0.17
Rv1258c 1407308 c.33G>T synonymous_variant 0.15
embR 1416699 p.Leu217Val missense_variant 1.0
embR 1417109 p.Arg80His missense_variant 0.12
embR 1417147 c.201C>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.13
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1473203 n.1358G>A non_coding_transcript_exon_variant 0.14
rrl 1473970 n.313G>T non_coding_transcript_exon_variant 0.17
rrl 1474544 n.887G>T non_coding_transcript_exon_variant 0.15
rrl 1475030 n.1373G>T non_coding_transcript_exon_variant 0.17
rrl 1475044 n.1387G>A non_coding_transcript_exon_variant 0.17
rrl 1475103 n.1446C>T non_coding_transcript_exon_variant 0.15
fabG1 1673412 c.-28G>A upstream_gene_variant 0.2
inhA 1673994 c.-208C>T upstream_gene_variant 0.15
inhA 1674257 p.Ser19* stop_gained 0.14
inhA 1674328 c.127C>A synonymous_variant 0.2
rpsA 1833405 c.-137A>G upstream_gene_variant 0.14
rpsA 1833832 c.291G>A synonymous_variant 0.11
rpsA 1833838 c.297G>C synonymous_variant 0.12
rpsA 1833841 c.300C>G synonymous_variant 0.12
rpsA 1833847 c.306C>G synonymous_variant 0.12
rpsA 1833856 c.315A>G synonymous_variant 0.13
rpsA 1833862 c.321G>T synonymous_variant 0.14
rpsA 1833874 c.333T>G synonymous_variant 0.15
rpsA 1833886 c.345C>G synonymous_variant 0.11
rpsA 1833928 c.387G>C synonymous_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918209 c.270C>A synonymous_variant 0.22
ndh 2101733 p.Phe437Ser missense_variant 0.11
ndh 2103226 c.-184C>A upstream_gene_variant 0.25
katG 2154206 p.Ala636Thr missense_variant 0.15
katG 2154248 p.Pro622Thr missense_variant 0.12
katG 2154405 c.1707G>T synonymous_variant 0.14
katG 2154626 p.Arg496Ser missense_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154964 p.Ser383Leu missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222079 c.1086A>G synonymous_variant 0.11
Rv1979c 2222146 p.Leu340Ser missense_variant 0.17
Rv1979c 2222170 p.Asp332Gly missense_variant 0.13
Rv1979c 2222359 p.Leu269Pro missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289345 c.-104G>T upstream_gene_variant 0.18
pncA 2289964 c.-723C>A upstream_gene_variant 0.12
pncA 2290069 c.-828C>A upstream_gene_variant 0.15
pncA 2290135 c.-899_-895dupATTAC upstream_gene_variant 0.33
kasA 2517928 c.-187A>G upstream_gene_variant 0.12
kasA 2518236 p.Ser41Asn missense_variant 0.2
kasA 2518797 p.Arg228Gln missense_variant 0.2
kasA 2519288 p.Gly392Ser missense_variant 1.0
folC 2747411 p.Ser63Ile missense_variant 0.33
pepQ 2860121 p.His100Tyr missense_variant 0.22
pepQ 2860536 c.-118A>G upstream_gene_variant 0.18
ribD 2986905 p.Leu23Ile missense_variant 0.12
ribD 2987132 p.Met98Ile missense_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 0.33
Rv2752c 3064668 c.1524G>T synonymous_variant 0.2
Rv2752c 3064737 p.Gln485His missense_variant 0.18
thyX 3067890 p.Ala19Asp missense_variant 0.22
thyA 3073841 p.Asn211Asp missense_variant 0.1
thyA 3074551 c.-80C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087176 c.357C>T synonymous_variant 0.5
Rv3083 3449084 p.Pro194Leu missense_variant 0.25
Rv3083 3449408 p.Asn302Ile missense_variant 0.12
Rv3083 3449489 p.Ile329Thr missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474259 p.Gly85Ser missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612892 c.225G>A synonymous_variant 0.25
Rv3236c 3613144 c.-28G>T upstream_gene_variant 0.14
Rv3236c 3613153 c.-37G>T upstream_gene_variant 0.13
fbiA 3640552 p.Thr4Ser missense_variant 0.29
fbiB 3640680 c.-855C>T upstream_gene_variant 0.13
fbiA 3640785 p.Gln81His missense_variant 0.15
fbiB 3641753 p.Leu73Phe missense_variant 0.29
fbiB 3642773 c.1239C>T synonymous_variant 0.22
alr 3840712 p.Ser237Pro missense_variant 0.11
rpoA 3877557 c.951C>A synonymous_variant 0.13
rpoA 3878484 c.24C>A synonymous_variant 0.12
ddn 3987082 p.Gly80Val missense_variant 0.12
clpC1 4038350 c.2355C>A synonymous_variant 0.17
clpC1 4038706 c.1998delC frameshift_variant 0.14
panD 4043918 p.Ala122Thr missense_variant 0.25
embC 4239701 c.-162C>A upstream_gene_variant 0.14
embC 4239970 c.108G>T synonymous_variant 0.25
embC 4240228 c.366G>T synonymous_variant 0.18
embC 4240823 p.Glu321* stop_gained 0.17
embC 4241441 p.Pro527Ser missense_variant 0.12
embC 4241730 p.Ala623Asp missense_variant 0.17
embC 4242347 p.Ala829Thr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242781 c.-452C>T upstream_gene_variant 0.17
embC 4243112 p.Gly1084Trp missense_variant 0.15
embA 4243154 c.-79C>A upstream_gene_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243610 c.378G>T synonymous_variant 0.29
embB 4246800 p.Gly96Val missense_variant 0.22
embB 4248301 p.Phe596Leu missense_variant 0.1
embB 4248674 p.Ser721Pro missense_variant 0.12
embB 4248681 p.Val723Ala missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269251 c.582delC frameshift_variant 0.13
ethA 4326017 p.Pro486Arg missense_variant 0.1
ethA 4326900 p.Pro192Ser missense_variant 0.29
ethR 4327645 p.Ala33Thr missense_variant 0.25
ethA 4328245 c.-772C>T upstream_gene_variant 0.18
whiB6 4338325 p.Ala66Val missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.92
gid 4407953 p.Pro84Thr missense_variant 0.18
gid 4408030 p.Leu58His missense_variant 0.67
gid 4408034 p.Glu57* stop_gained 0.5