TB-Profiler result

Run: SRR11972265
Summary

Run ID: SRR11972265

Sample name:

Date: 03-04-2023 05:34:09

Number of reads: 626342

Percentage reads mapped: 99.53

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 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5083 c.-157C>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7534 p.Ala78Val missense_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575508 p.Thr54Ile missense_variant 0.13
mshA 575900 p.Asn185Tyr missense_variant 0.25
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759713 c.-94C>A upstream_gene_variant 0.11
rpoB 759945 p.Leu47Phe missense_variant 0.12
rpoB 760657 p.Glu284Val missense_variant 1.0
rpoB 761384 c.1578C>A synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 1.0
rpoC 764429 c.1060C>T synonymous_variant 0.19
rpoC 766270 c.2901G>A synonymous_variant 0.18
rpoC 767041 c.3672G>A synonymous_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
mmpL5 778044 p.Ala146Val missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305019 p.Ala697Thr missense_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472736 n.891G>A non_coding_transcript_exon_variant 0.18
rrl 1474160 n.503C>T non_coding_transcript_exon_variant 0.12
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.13
rrl 1475004 n.1347C>A non_coding_transcript_exon_variant 0.22
rrl 1475779 n.2122A>G non_coding_transcript_exon_variant 0.12
inhA 1673791 c.-411C>A upstream_gene_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834354 c.813G>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918308 c.369C>T synonymous_variant 0.12
ndh 2102200 c.843G>T synonymous_variant 0.12
ndh 2102225 p.Cys273Tyr missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155405 p.Asn236Ser missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222494 p.Ala224Val missense_variant 0.12
Rv1979c 2222883 c.282C>T synonymous_variant 0.14
Rv1979c 2223052 p.Glu38Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289273 c.-32C>T upstream_gene_variant 0.14
pncA 2289921 c.-680A>G upstream_gene_variant 0.12
ahpC 2726405 c.213C>T synonymous_variant 0.12
folC 2747437 p.Met54Ile missense_variant 1.0
folC 2747476 c.123C>T synonymous_variant 0.14
ribD 2986921 p.Leu28Pro missense_variant 0.11
Rv2752c 3064782 c.1410G>T synonymous_variant 0.13
Rv2752c 3065633 p.Gly187Ser missense_variant 0.12
thyX 3067212 p.Pro245Gln missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449417 p.Leu305Gln missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612113 c.1003delG frameshift_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612933 p.Ala62Thr missense_variant 0.2
fbiA 3640934 p.Ala131Asp missense_variant 0.2
fbiB 3641891 c.357G>A synonymous_variant 0.22
rpoA 3877588 p.Ser307* stop_gained 0.18
rpoA 3878060 p.Val150Met missense_variant 0.11
clpC1 4038166 p.Ala847Thr missense_variant 0.12
clpC1 4039621 c.1084C>T synonymous_variant 0.12
clpC1 4040410 c.294delT frameshift_variant 0.12
embC 4241183 p.Thr441Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244513 c.1281C>T synonymous_variant 0.13
embB 4246241 c.-273G>C upstream_gene_variant 0.12
embB 4246575 p.Ala21Val missense_variant 0.15
embB 4246623 p.Gly37Asp missense_variant 0.12
embB 4246762 c.249G>T synonymous_variant 0.11
embB 4248794 p.Ala761Thr missense_variant 0.14
aftB 4267322 c.1515C>T synonymous_variant 0.13
aftB 4267533 p.Met435Lys missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326225 p.Val417Met missense_variant 0.11
ethA 4326713 p.Gln254Pro missense_variant 1.0
ethA 4328424 c.-951C>T upstream_gene_variant 0.14
whiB6 4338250 p.Ala91Val missense_variant 0.12
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 4408027 p.Leu59Pro missense_variant 0.14