TB-Profiler result

Run: SRR11972220
Summary

Run ID: SRR11972220

Sample name:

Date: 03-04-2023 05:32:25

Number of reads: 307603

Percentage reads mapped: 99.45

Strain: lineage2.2.1.1

Drug-resistance: HR-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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.99
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
katG 2154422 c.1689delC frameshift_variant 0.17 isoniazid
pncA 2288817 p.Thr142Met missense_variant 0.14 pyrazinamide
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8414 c.1113C>T synonymous_variant 0.15
gyrA 9066 p.Arg589Gly missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620203 p.Val105Leu missense_variant 0.29
ccsA 620457 c.567C>A synonymous_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761198 c.1392G>T synonymous_variant 0.15
rpoB 761601 c.1798delC frameshift_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765474 p.Glu702Gly missense_variant 0.22
rpoC 766446 p.Gly1026Val missense_variant 0.2
rpoC 767065 c.3696G>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 776787 p.Glu565Gly missense_variant 0.12
mmpL5 776957 p.Gln508His missense_variant 0.13
mmpL5 777039 p.Val481Glu missense_variant 0.14
mmpL5 777119 p.His454Gln missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.18
mmpL5 777136 p.Met449Leu missense_variant 0.18
mmpL5 777142 p.Val447Met missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781612 p.Lys18Arg missense_variant 0.11
fbiC 1304738 p.Gly603Val missense_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475194 n.1537C>T non_coding_transcript_exon_variant 0.2
inhA 1674426 c.225C>A synonymous_variant 0.17
inhA 1674984 c.783C>T synonymous_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834295 p.Val252Ile missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102445 p.Ala200Thr missense_variant 0.18
ndh 2102759 p.Ala95Val missense_variant 0.25
katG 2154618 c.1494C>T synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155930 p.Ala61Val missense_variant 0.15
katG 2156416 c.-305G>T upstream_gene_variant 0.2
PPE35 2167916 c.2697C>T synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169384 p.Gly410Val missense_variant 0.25
PPE35 2169986 p.Leu209Ile missense_variant 0.13
PPE35 2170503 p.Glu37Gly missense_variant 0.12
Rv1979c 2222191 p.Arg325Gln missense_variant 0.13
Rv1979c 2222872 p.His98Arg missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518781 p.Pro223Thr missense_variant 0.22
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2715408 c.-76G>T upstream_gene_variant 0.18
pepQ 2859437 p.Val328Leu missense_variant 0.15
ribD 2987594 c.756C>T synonymous_variant 0.2
Rv2752c 3064945 p.Pro416Gln missense_variant 0.2
Rv2752c 3065129 c.1063C>T synonymous_variant 0.18
Rv2752c 3065906 c.286C>T synonymous_variant 0.13
thyA 3074576 c.-105C>T upstream_gene_variant 0.5
ald 3086638 c.-182G>C upstream_gene_variant 0.17
ald 3086723 c.-97T>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339330 c.213G>C synonymous_variant 0.25
Rv3083 3448541 p.Gly13Asp missense_variant 0.18
Rv3083 3449895 p.Met464Ile missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475082 p.Trp359Ser missense_variant 0.29
fprA 3475198 p.Phe398Leu missense_variant 0.18
whiB7 3568573 p.Leu36Pro missense_variant 0.18
whiB7 3568692 c.-13G>A upstream_gene_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641720 c.186G>T synonymous_variant 0.25
alr 3840252 p.Val390Ala missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.23
clpC1 4039645 p.His354Asp missense_variant 0.12
clpC1 4040800 c.-96A>C upstream_gene_variant 0.12
embC 4240828 c.966G>A synonymous_variant 0.25
embC 4241587 c.1727delT frameshift_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246003 p.Asn924Ile missense_variant 0.2
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248887 p.Gly792Ser missense_variant 0.13
embB 4248924 p.Met804Lys missense_variant 0.17
embB 4249489 p.Leu992Phe missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326217 c.1257C>T synonymous_variant 0.33
ethA 4326478 p.Glu332Asp missense_variant 0.2
whiB6 4338594 c.-73T>G upstream_gene_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