TB-Profiler result

Run: SRR11972221
Summary

Run ID: SRR11972221

Sample name:

Date: 03-04-2023 05:32:30

Number of reads: 311067

Percentage reads mapped: 96.98

Strain: lineage2.2.1

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 0.95
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.96
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.96
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
rpsL 781687 p.Lys43Arg missense_variant 0.94 streptomycin
katG 2154812 p.Gln434* stop_gained 0.15 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.15 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 6576 p.Arg446Pro missense_variant 0.13
gyrA 6646 c.-656C>T upstream_gene_variant 0.12
gyrB 7049 p.Glu604Lys missense_variant 0.18
gyrA 7338 p.Asp13Asn missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7512 p.Ala71Thr missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 0.83
gyrA 7624 p.Pro108Leu missense_variant 0.12
gyrA 7832 c.531G>T synonymous_variant 0.14
gyrA 8116 p.Thr272Ile missense_variant 0.17
gyrA 9143 c.1842T>C synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490926 c.144C>T synonymous_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.89
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760009 p.Ala68Gly missense_variant 0.18
rpoB 761629 p.Gln608Arg missense_variant 0.25
rpoB 761901 p.Gly699Ser missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764732 p.Phe455Val missense_variant 0.2
rpoC 765275 p.Arg636Trp missense_variant 0.18
rpoC 766493 p.Gly1042Cys missense_variant 0.15
rpoC 766669 c.3300C>G synonymous_variant 0.13
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 776807 c.1674G>T synonymous_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801075 c.267G>A synonymous_variant 0.2
rplC 801274 p.Thr156Pro missense_variant 0.17
Rv1258c 1406505 p.Ala279Val missense_variant 0.14
Rv1258c 1406526 p.Leu272Gln missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1460862 c.-183T>C upstream_gene_variant 0.22
atpE 1461032 c.-13G>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.15
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.16
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.14
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.14
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.13
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.13
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.13
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.14
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.13
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.12
rrl 1474632 n.975G>A non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834523 p.Glu328Lys missense_variant 0.22
tlyA 1917808 c.-132C>A upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169394 p.Ala407Ser missense_variant 0.12
PPE35 2169397 p.Gly406Ser missense_variant 0.12
PPE35 2169412 p.Thr401Ala missense_variant 0.11
PPE35 2169413 c.1200T>C synonymous_variant 0.11
PPE35 2169743 c.870G>A synonymous_variant 0.12
PPE35 2169851 c.762C>T synonymous_variant 0.14
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2169969 p.Gly215Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290067 c.-826C>A upstream_gene_variant 0.29
kasA 2518075 c.-40C>A upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 0.17
kasA 2518150 c.36C>T synonymous_variant 0.17
kasA 2518879 c.765A>G synonymous_variant 0.18
kasA 2518882 c.768C>A synonymous_variant 0.18
kasA 2519055 p.Ala314Val missense_variant 0.29
kasA 2519140 c.1026G>C synonymous_variant 0.25
kasA 2519143 c.1029G>C synonymous_variant 0.25
kasA 2519153 p.Ile347Val missense_variant 0.29
eis 2714846 p.Val163Ile missense_variant 1.0
pepQ 2859498 c.921C>T synonymous_variant 0.2
pepQ 2859692 p.Ala243Thr missense_variant 0.17
pepQ 2859708 p.Phe237Leu missense_variant 0.17
pepQ 2860170 c.249G>A synonymous_variant 0.29
Rv2752c 3064545 c.1647G>A synonymous_variant 0.25
Rv2752c 3066055 p.Gly46Asp missense_variant 0.14
thyX 3067640 c.306G>A synonymous_variant 0.18
thyA 3073936 p.Ala179Val missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339269 p.Ala51Val missense_variant 0.2
Rv3083 3449221 p.Tyr240His missense_variant 0.15
Rv3083 3449286 p.Trp261* stop_gained 0.14
Rv3083 3449687 p.Trp395* stop_gained 0.15
Rv3083 3449794 c.1291C>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.82
fprA 3474069 c.65delT frameshift_variant 0.17
fprA 3474337 p.Met111Leu missense_variant 0.12
Rv3236c 3612758 p.Gly120Val missense_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613016 p.Pro34Leu missense_variant 0.22
fbiA 3640456 c.-87G>A upstream_gene_variant 0.15
fbiB 3641814 p.Ile94Phe missense_variant 0.2
fbiB 3641954 c.420C>T synonymous_variant 0.29
alr 3840702 p.Thr240Ile missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.31
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4039654 p.Thr351Ser missense_variant 0.2
embC 4241125 c.1263G>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244507 c.1275G>T synonymous_variant 1.0
embA 4245465 p.Pro745Ser missense_variant 0.2
embA 4245881 p.Asp883Glu missense_variant 0.22
embB 4248115 c.1602C>T synonymous_variant 0.88
embB 4249257 p.Arg915Gln missense_variant 0.14
embB 4249384 c.2871G>A synonymous_variant 0.17
embB 4249739 p.Ala1076Thr missense_variant 0.23
aftB 4267000 p.Cys613Arg missense_variant 0.18
aftB 4267351 p.Met496Leu missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267834 p.His335Tyr missense_variant 0.22
aftB 4269222 c.-386T>C upstream_gene_variant 0.29
ubiA 4269879 c.-46C>T upstream_gene_variant 0.25
ethA 4326713 p.Gln254Pro missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338673 c.-152G>A upstream_gene_variant 0.13
gid 4407588 c.615A>G synonymous_variant 0.5
gid 4407927 p.Glu92Asp missense_variant 1.0