TB-Profiler result

Run: SRR6045473
Summary

Run ID: SRR6045473

Sample name:

Date: 04-04-2023 11:59:56

Number of reads: 523167

Percentage reads mapped: 98.65

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
gyrB 6536 p.Thr433Ala missense_variant 0.12
gyrB 6930 p.Ala564Val missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7462 p.Arg54Leu missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7958 c.657C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575989 c.642C>T synonymous_variant 0.17
ccsA 619814 c.-77G>T upstream_gene_variant 1.0
ccsA 620122 p.Arg78Trp missense_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763649 p.His94Asn missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777471 p.Val337Ala missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305411 c.2481C>T synonymous_variant 1.0
Rv1258c 1406316 p.Gln342Arg missense_variant 0.13
embR 1416501 p.Ala283Thr missense_variant 0.11
rrs 1471648 n.-198A>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834435 c.894G>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102818 c.225G>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 1.0
PPE35 2169047 p.Ile522Val missense_variant 1.0
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 1.0
PPE35 2169741 p.Asn291Ser missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289351 c.-110C>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518174 c.60A>G synonymous_variant 0.18
kasA 2518190 p.Ser26Ala missense_variant 0.2
kasA 2518199 p.Ile29Val missense_variant 0.18
kasA 2518222 c.108G>A synonymous_variant 0.18
kasA 2518223 c.109_111delTTGinsCTC synonymous_variant 0.18
kasA 2518234 c.120G>A synonymous_variant 0.2
kasA 2518248 p.Ala45Val missense_variant 0.15
kasA 2518480 c.366T>C synonymous_variant 0.1
kasA 2518483 c.369C>G synonymous_variant 0.11
kasA 2518504 c.390T>C synonymous_variant 0.14
kasA 2518506 p.Ala131Glu missense_variant 0.17
kasA 2518519 c.405G>C synonymous_variant 0.2
kasA 2518528 c.414C>G synonymous_variant 0.25
kasA 2518540 c.426T>G synonymous_variant 0.25
eis 2715020 p.His105Tyr missense_variant 0.17
eis 2715063 c.270G>T synonymous_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747396 c.202delC frameshift_variant 0.13
pepQ 2859422 p.Arg333Cys missense_variant 0.15
pepQ 2860147 p.Gly91Asp missense_variant 0.12
Rv2752c 3066150 c.42C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087688 p.Val290Ala missense_variant 0.15
fbiD 3339515 p.Arg133Leu missense_variant 0.18
Rv3083 3449227 p.Phe242Leu missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612621 c.496T>C synonymous_variant 0.14
fbiB 3640728 c.-807G>C upstream_gene_variant 0.11
alr 3841612 c.-193_-192insC upstream_gene_variant 0.13
rpoA 3877896 c.612G>T synonymous_variant 0.17
ddn 3987243 p.Gln134* stop_gained 0.12
clpC1 4039169 p.Glu512Asp missense_variant 0.11
clpC1 4039172 c.1533A>G synonymous_variant 0.11
clpC1 4039178 c.1527G>C synonymous_variant 0.12
clpC1 4039183 c.1522T>C synonymous_variant 0.14
clpC1 4039187 c.1518G>C synonymous_variant 0.14
clpC1 4039190 c.1515C>G synonymous_variant 0.15
clpC1 4039906 p.Glu267Lys missense_variant 0.12
clpC1 4040579 c.126A>G synonymous_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242649 c.-584G>C upstream_gene_variant 0.33
embC 4242702 p.Ala947Val missense_variant 0.13
embC 4242770 p.Thr970Ser missense_variant 0.15
embA 4244417 c.1185G>A synonymous_variant 0.17
embA 4244984 c.1752G>A synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407540 c.663A>T synonymous_variant 0.13
gid 4407588 c.615A>G synonymous_variant 1.0