TB-Profiler result

Run: SRR21277521
Summary

Run ID: SRR21277521

Sample name:

Date: 04-04-2023 01:19:16

Number of reads: 14222370

Percentage reads mapped: 97.46

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 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
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575893 c.546C>T synonymous_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576223 c.876G>T synonymous_variant 0.12
mshA 576495 p.Asp383Val missense_variant 0.25
mshA 576523 c.1176G>T synonymous_variant 0.22
mshA 576625 c.1278C>T synonymous_variant 0.18
ccsA 619694 c.-197C>A upstream_gene_variant 0.12
ccsA 619838 c.-53G>T upstream_gene_variant 0.1
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766083 p.Ala905Glu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777311 c.1170C>T synonymous_variant 0.17
mmpL5 777318 p.Arg388Leu missense_variant 0.25
mmpL5 777371 c.1110C>A synonymous_variant 0.11
mmpR5 779208 p.Met73Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303114 p.Ala62Thr missense_variant 0.13
fbiC 1303927 p.Ala333Thr missense_variant 0.12
fbiC 1303941 c.1011G>A synonymous_variant 0.12
Rv1258c 1406308 p.Arg345Cys missense_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.95
tlyA 1918104 c.165G>T synonymous_variant 0.11
tlyA 1918578 c.639G>A synonymous_variant 0.18
tlyA 1918591 c.652C>T synonymous_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155744 p.Gly123Val missense_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170100 c.513G>A synonymous_variant 0.1
PPE35 2170363 p.Glu84* stop_gained 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746350 p.Leu417Met missense_variant 0.18
folC 2746600 c.999C>T synonymous_variant 0.2
pepQ 2859603 p.Gly272Phe missense_variant 0.14
pepQ 2859606 c.813G>A synonymous_variant 0.11
pepQ 2859611 p.Leu270Met missense_variant 0.12
pepQ 2859925 p.Pro165Leu missense_variant 0.4
pepQ 2859957 p.Leu154Ile missense_variant 0.2
pepQ 2860582 c.-164A>T upstream_gene_variant 0.13
thyX 3067232 c.714C>T synonymous_variant 0.13
thyX 3067414 p.Ala178Ser missense_variant 0.11
thyX 3067427 c.519G>T synonymous_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087309 p.Pro164Thr missense_variant 0.11
ald 3087313 p.Gly165Asp missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
fbiB 3642244 p.Ala237Val missense_variant 0.15
fbiB 3642359 c.825C>A synonymous_variant 0.1
alr 3841191 p.Val77Asp missense_variant 0.29
alr 3841546 c.-126C>A upstream_gene_variant 1.0
alr 3841568 c.-148G>A upstream_gene_variant 1.0
alr 3841570 c.-151delA upstream_gene_variant 1.0
alr 3841574 c.-154T>G upstream_gene_variant 1.0
alr 3841578 c.-158G>T upstream_gene_variant 1.0
alr 3841582 c.-162A>G upstream_gene_variant 1.0
alr 3841584 c.-164C>A upstream_gene_variant 1.0
alr 3841589 c.-170delG upstream_gene_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
clpC1 4038187 p.Ala840Ser missense_variant 0.1
embC 4240641 p.Arg260Leu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243503 p.Ser91Thr missense_variant 0.14
embA 4243613 c.381C>T synonymous_variant 0.22
embA 4243886 p.Met218Ile missense_variant 0.12
embB 4246681 c.168C>A synonymous_variant 0.14
embB 4247028 p.Leu172Arg missense_variant 0.38
embB 4247855 p.Gly448Ser missense_variant 0.12
embB 4248594 p.Gly694Asp missense_variant 0.16
embB 4248599 p.Gly696Trp missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267669 p.Ala390Thr missense_variant 0.17
aftB 4267928 c.909G>C synonymous_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