TB-Profiler result

Run: SRR4033862
Summary

Run ID: SRR4033862

Sample name:

Date: 04-04-2023 06:23:37

Number of reads: 566542

Percentage reads mapped: 99.55

Strain: lineage2.2.1

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 0.99
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
ethA 4326326 c.1147delA frameshift_variant 0.12 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 5814 p.Arg192His missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7909 p.Trp203* stop_gained 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575510 p.Ser55Pro missense_variant 0.27
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620016 c.126C>A synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761482 p.Ala559Gly missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763958 c.591delT frameshift_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801142 p.Val112Leu missense_variant 0.25
fbiC 1305208 p.Gly760Trp missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471994 n.149G>A non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.22
rrl 1475355 n.1698C>A non_coding_transcript_exon_variant 0.25
fabG1 1673770 p.Ala111Thr missense_variant 0.12
fabG1 1673821 p.Gln128* stop_gained 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834716 c.1179delC frameshift_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102697 c.345delG frameshift_variant 0.14
ndh 2102863 c.180C>T synonymous_variant 0.17
ndh 2103208 c.-166G>A upstream_gene_variant 0.17
katG 2154241 p.Met624Lys missense_variant 0.15
katG 2154720 c.1392A>G synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154785 p.Pro443Thr missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167993 p.Thr874Ala missense_variant 0.17
PPE35 2169208 c.1404delC frameshift_variant 0.13
PPE35 2169320 p.Leu431Phe missense_variant 0.22
Rv1979c 2222836 p.Ala110Asp missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725931 c.-261delG upstream_gene_variant 0.12
folC 2747066 p.Gly178Asp missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087295 p.Leu159Pro missense_variant 0.18
ald 3087502 p.Ala228Val missense_variant 0.18
fprA 3473914 c.-93G>C upstream_gene_variant 0.22
fprA 3473951 c.-56C>A upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568478 p.Gly68Cys missense_variant 0.13
Rv3236c 3611961 c.1156T>C stop_lost&splice_region_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641332 p.Gly264Arg missense_variant 1.0
fbiB 3641645 c.111A>C synonymous_variant 0.2
fbiB 3641832 p.Gly100Trp missense_variant 0.2
fbiB 3642123 p.Glu197* stop_gained 0.25
fbiB 3642153 p.Gly207Cys missense_variant 0.25
alr 3841365 p.Gly19Asp missense_variant 0.15
rpoA 3878641 c.-134C>G upstream_gene_variant 0.43
clpC1 4040521 p.Gln62* stop_gained 0.11
embC 4241813 p.Ser651Pro missense_variant 0.18
embC 4242072 p.Gly737Asp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244449 p.Ala406Val missense_variant 0.14
embB 4246241 c.-273G>A upstream_gene_variant 0.2
embB 4248232 c.1719G>A synonymous_variant 0.17
embB 4249132 c.2619G>A synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268890 c.-54C>T upstream_gene_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 1.0