TB-Profiler result

Run: SRR6046574
Summary

Run ID: SRR6046574

Sample name:

Date: 04-04-2023 12:19:14

Number of reads: 785211

Percentage reads mapped: 67.01

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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 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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764724 p.Phe452Ser missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289072 p.His57Arg missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
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 6583 c.-719G>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9725 p.Glu808Asp missense_variant 0.17
fgd1 491623 p.Ala281Ser missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.97
mshA 576259 p.Ser304Arg missense_variant 0.29
ccsA 620559 c.669A>G synonymous_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620817 c.927C>T synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764024 p.Leu219Met missense_variant 0.17
rpoC 764307 p.Val313Glu missense_variant 0.13
rpoC 766393 c.3024C>A synonymous_variant 0.12
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 777508 p.Ser325Arg missense_variant 0.94
mmpL5 778344 p.Leu46Pro missense_variant 0.13
mmpR5 779353 p.Leu122Val missense_variant 0.18
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
embR 1417002 p.Val116Leu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476706 n.3049C>T non_coding_transcript_exon_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918256 p.Ala106Asp missense_variant 0.11
ndh 2101975 c.1068G>A synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154883 p.Lys410Arg missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169927 p.Asn229Ser missense_variant 0.17
Rv1979c 2222201 p.Gly322Arg missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223297 c.-133G>T upstream_gene_variant 0.11
kasA 2518809 p.Lys232Arg missense_variant 0.12
kasA 2518864 c.750G>C synonymous_variant 0.12
kasA 2518879 c.765A>G synonymous_variant 0.11
kasA 2518882 c.768C>A synonymous_variant 0.12
kasA 2518959 p.Ala282Asp missense_variant 0.13
eis 2714404 p.Tyr310Cys missense_variant 0.95
eis 2714779 p.Gln185Arg missense_variant 0.18
eis 2715495 c.-163G>A upstream_gene_variant 0.22
folC 2746227 p.Gly458Arg missense_variant 0.2
Rv2752c 3064597 p.Gly532Val missense_variant 0.15
Rv2752c 3065238 p.Met318Ile missense_variant 0.11
Rv2752c 3065314 p.Glu293Gly missense_variant 0.12
Rv2752c 3065420 p.Arg258* stop_gained 0.15
thyX 3067235 c.711C>T synonymous_variant 0.15
thyX 3067365 p.His194Arg missense_variant 0.18
thyX 3068015 c.-70T>C upstream_gene_variant 0.15
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338970 c.-148C>T upstream_gene_variant 0.17
fbiD 3339035 c.-83G>A upstream_gene_variant 0.25
fbiD 3339327 c.210T>C synonymous_variant 0.11
Rv3083 3449026 p.Tyr175His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475057 p.Ser351Gly missense_variant 0.22
fprA 3475061 p.Pro352His missense_variant 0.22
fprA 3475271 p.His422Pro missense_variant 0.17
Rv3236c 3612704 p.Glu138Gly missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612902 p.Ala72Val missense_variant 0.22
fbiB 3642786 p.Trp418Gly missense_variant 0.14
rpoA 3878285 c.222delC frameshift_variant 0.15
rpoA 3878670 c.-163T>C upstream_gene_variant 0.29
clpC1 4038288 p.Asn806Ser missense_variant 0.11
clpC1 4040329 p.Lys126Gln missense_variant 0.15
panD 4044173 p.Asp37Asn missense_variant 0.18
panD 4044179 p.Ala35Thr missense_variant 0.18
embC 4240990 c.1128A>C synonymous_variant 0.33
embC 4242255 p.Pro798Arg missense_variant 0.2
embC 4242577 p.Gln905His missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242677 p.Thr939Pro missense_variant 0.15
embC 4242730 p.His956Gln missense_variant 0.17
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244269 p.Arg346Leu missense_variant 0.15
embA 4246249 p.Arg1006Gln missense_variant 0.13
embB 4246818 p.Ala102Gly missense_variant 0.14
embB 4249285 p.Glu924Asp missense_variant 0.15
embB 4249768 c.3255C>A synonymous_variant 0.11
aftB 4267636 p.Arg401Trp missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267842 p.Asp332Gly missense_variant 0.15
aftB 4268425 p.Gly138Arg missense_variant 0.1
ethA 4327472 c.2T>G start_lost 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 0.14
whiB6 4338371 p.Thr51Pro missense_variant 1.0
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 4408049 p.Cys52Arg missense_variant 0.16