TB-Profiler result

Run: SRR21277514

Summary

Run ID: SRR21277514

Sample name:

Date: 04-04-2023 01:19:36

Number of reads: 13147310

Percentage reads mapped: 97.8

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
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 6040 c.801C>A synonymous_variant 1.0
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 575907 p.Ala187Val missense_variant 0.98
mshA 576583 c.1236A>C synonymous_variant 1.0
ccsA 620125 p.Gly79Ser missense_variant 0.25
ccsA 620148 c.258G>T synonymous_variant 0.1
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761277 p.Ile491Val missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763949 p.Arg194Trp missense_variant 0.11
rpoC 765145 c.1776C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777311 c.1170C>T synonymous_variant 0.22
mmpL5 777354 p.Val376Glu missense_variant 0.2
mmpL5 777358 c.1123C>A synonymous_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303116 c.186C>A synonymous_variant 0.2
fbiC 1304446 p.Pro506Thr missense_variant 0.13
fbiC 1305501 c.2571G>A splice_region_variant&stop_retained_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406991 p.Gly117Val missense_variant 0.11
Rv1258c 1407014 c.327G>A synonymous_variant 0.22
Rv1258c 1407534 c.-194C>T upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833856 c.315A>G synonymous_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.97
tlyA 1917987 c.48G>A synonymous_variant 0.22
tlyA 1918579 p.Arg214Trp missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155744 p.Gly123Val missense_variant 0.27
katG 2155758 c.354C>A synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170061 c.552C>T synonymous_variant 0.19
PPE35 2170064 c.549G>T synonymous_variant 0.18
PPE35 2170079 c.534G>A synonymous_variant 0.15
PPE35 2170401 p.Pro71Gln missense_variant 0.12
Rv1979c 2222270 p.Thr299Ala missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519042 p.Ala310Thr missense_variant 0.12
folC 2746329 p.Arg424Trp missense_variant 0.12
folC 2746333 c.1266C>A synonymous_variant 0.13
pepQ 2859605 p.Gly272Trp missense_variant 0.18
pepQ 2859914 p.Glu169* stop_gained 0.12
pepQ 2860147 p.Gly91Val missense_variant 0.12
pepQ 2860589 c.-171G>T upstream_gene_variant 0.56
thyX 3067238 c.708C>T synonymous_variant 0.12
thyX 3067454 c.492C>A synonymous_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087310 p.Pro164His missense_variant 0.12
fbiD 3339332 p.Ala72Val missense_variant 0.1
fbiD 3339586 p.Ala157Thr missense_variant 0.12
fbiD 3339737 p.Thr207Ile missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641913 p.Ala127Thr missense_variant 0.1
fbiB 3642230 c.696G>A synonymous_variant 0.13
fbiB 3642249 p.Asp239Tyr missense_variant 0.12
alr 3841034 p.Gln129His missense_variant 0.11
alr 3841101 c.319delG frameshift_variant 0.11
embC 4242036 p.Gln725Arg missense_variant 1.0
embC 4242398 p.Ala846Thr missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244236 p.Cys335Tyr missense_variant 0.12
embA 4244545 p.Ala438Asp missense_variant 0.22
embA 4244570 c.1338C>T synonymous_variant 0.29
embA 4244882 p.Trp550Cys missense_variant 0.11
embB 4247110 c.597G>T synonymous_variant 0.12
embB 4247867 p.Val452Met missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4328472 c.-999G>T upstream_gene_variant 0.11
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