TB-Profiler result

Run: SRR6257068

Summary

Run ID: SRR6257068

Sample name:

Date: 04-04-2023 13:25:01

Number of reads: 798856

Percentage reads mapped: 97.79

Strain: lineage2.2.1

Drug-resistance: Sensitive


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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
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 7932 p.Asp211Tyr missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575267 c.-81G>A upstream_gene_variant 0.12
mshA 575853 p.Trp169Leu missense_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761718 p.Ala638Thr missense_variant 0.22
rpoC 762470 c.-900G>A upstream_gene_variant 0.14
rpoB 762918 p.Arg1038Ser missense_variant 0.15
rpoB 762935 p.Tyr1043* stop_gained 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763097 p.Tyr1097* stop_gained 0.12
rpoC 763670 p.Val101Phe missense_variant 0.22
rpoC 763853 p.Val162Ile missense_variant 0.18
rpoC 765818 p.Leu817Met missense_variant 0.14
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.21
mmpL5 776021 c.2460G>C synonymous_variant 0.21
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777173 c.1308C>T synonymous_variant 0.12
mmpL5 777725 c.756C>T synonymous_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303511 p.Gly194Asp missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8
atpE 1461052 p.Pro3Leu missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474218 n.561T>C non_coding_transcript_exon_variant 0.12
rrl 1474649 n.992A>G non_coding_transcript_exon_variant 0.17
rrl 1474759 n.1102A>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
inhA 1674714 c.513C>A synonymous_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102420 p.Lys208Arg missense_variant 0.17
katG 2154044 p.Thr690Ser missense_variant 0.12
katG 2154566 p.Lys516* stop_gained 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.27
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168905 p.Ile570Phe missense_variant 0.12
PPE35 2169269 c.1344A>G synonymous_variant 0.23
PPE35 2169272 c.1341C>G synonymous_variant 0.23
PPE35 2169278 c.1335T>C synonymous_variant 0.22
PPE35 2169281 c.1332T>G synonymous_variant 0.25
PPE35 2169287 c.1326T>C synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.48
PPE35 2170566 p.Phe16Tyr missense_variant 0.16
PPE35 2170623 c.-11G>A upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518809 p.Lys232Arg missense_variant 0.24
kasA 2518839 p.Ala242Gly missense_variant 0.17
kasA 2518879 c.765A>G synonymous_variant 0.27
kasA 2518882 c.768C>A synonymous_variant 0.29
kasA 2518896 c.783_784delGT frameshift_variant 0.15
kasA 2519140 c.1026G>C synonymous_variant 0.18
kasA 2519143 c.1029G>C synonymous_variant 0.18
eis 2714955 c.378C>T synonymous_variant 1.0
folC 2746660 c.938delT frameshift_variant 0.29
folC 2747361 p.Arg80Ser missense_variant 0.18
Rv2752c 3065377 p.Val272Ala missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087413 c.594C>T synonymous_variant 0.14
fbiD 3339630 c.513C>T synonymous_variant 1.0
Rv3083 3448907 p.Tyr135Cys missense_variant 0.14
Rv3083 3449041 p.Val180Ile missense_variant 0.15
Rv3083 3449061 c.558C>G synonymous_variant 0.18
Rv3083 3449064 c.561A>C synonymous_variant 0.18
Rv3083 3449456 c.955_958delGATC frameshift_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612568 c.549G>T synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641958 c.431_448delTCGCCGTGGTCATCACCG disruptive_inframe_deletion 0.2
fbiB 3642257 c.723C>T synonymous_variant 0.18
fbiB 3642363 p.Glu277Lys missense_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 0.35
clpC1 4039498 p.Ile403Val missense_variant 0.14
clpC1 4039508 c.1197G>C synonymous_variant 0.13
clpC1 4039526 c.1179G>C synonymous_variant 0.2
embC 4239780 c.-83G>A upstream_gene_variant 0.15
embC 4240801 c.939C>T synonymous_variant 0.17
embC 4240803 p.Tyr314Phe missense_variant 0.17
embC 4241118 c.1257_1258insGGCAGC conservative_inframe_insertion 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243157 c.-76G>C upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244102 c.870A>G synonymous_variant 0.14
embA 4244579 c.1347C>A synonymous_variant 0.15
embA 4245672 p.Gly814Arg missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4247830 c.1317A>G synonymous_variant 0.12
embB 4248116 p.Gly535Ser missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4326925 c.-624A>G upstream_gene_variant 0.18
ethR 4326934 c.-615C>G upstream_gene_variant 0.2
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_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