TB-Profiler result

Run: SRR21735256
Summary

Run ID: SRR21735256

Sample name:

Date: 04-04-2023 03:22:52

Number of reads: 338932

Percentage reads mapped: 96.52

Strain: lineage1

Drug-resistance: Other

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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
lineage1 Indo-Oceanic EAI RD239 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
rpsA 1834962 p.Arg474Leu missense_variant 0.29 pyrazinamide
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 5595 p.Gly119Asp missense_variant 0.33
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 0.5
gyrB 6827 p.Met530Val missense_variant 0.5
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7532 c.231T>C synonymous_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7624 p.Pro108Gln missense_variant 0.18
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9091 p.Ala597Val missense_variant 0.33
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9689 c.2388G>A synonymous_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575716 c.369C>T synonymous_variant 0.18
mshA 576009 p.Ala221Val missense_variant 0.4
rpoB 763083 p.Arg1093Ser missense_variant 1.0
rpoB 763236 p.Gly1144Ser missense_variant 0.5
rpoC 763399 c.30C>T synonymous_variant 0.4
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763920 p.Leu184Pro missense_variant 0.5
rpoC 765753 p.Asp795Gly missense_variant 0.67
rpoC 765819 p.Leu817Pro missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777608 c.873C>A synonymous_variant 0.4
mmpL5 777652 p.Tyr277His missense_variant 0.4
mmpR5 778409 c.-581G>A upstream_gene_variant 0.67
mmpS5 779669 c.-764C>T upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303061 p.Ala44Val missense_variant 0.4
fbiC 1303261 p.Pro111Ser missense_variant 0.5
fbiC 1303265 p.Gly112Asp missense_variant 0.67
fbiC 1303553 p.Ala208Val missense_variant 0.5
fbiC 1305070 p.Asp714Tyr missense_variant 0.29
fbiC 1305396 c.2466C>T synonymous_variant 0.29
Rv1258c 1406738 c.603C>T synonymous_variant 0.5
Rv1258c 1406912 c.429C>T synonymous_variant 0.29
embR 1417467 c.-120G>A upstream_gene_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673986 p.Pro183Thr missense_variant 0.2
inhA 1674498 c.297G>A synonymous_variant 0.25
rpsA 1834336 c.795C>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918520 p.Pro194Leu missense_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155907 p.Ala69Thr missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168395 p.Ser740Gly missense_variant 0.4
PPE35 2168623 p.Ala664Thr missense_variant 0.67
PPE35 2170400 c.213G>C synonymous_variant 0.17
Rv1979c 2222020 p.Arg382Gln missense_variant 0.67
Rv1979c 2222266 p.Phe300Tyr missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222328 c.837G>A synonymous_variant 0.33
Rv1979c 2222469 c.696C>T synonymous_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289460 c.-219G>T upstream_gene_variant 1.0
pncA 2290225 c.-984C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518353 p.Met80Lys missense_variant 0.25
kasA 2518903 c.789C>T synonymous_variant 0.22
kasA 2519065 c.951C>A synonymous_variant 0.5
eis 2714249 p.Gly362Arg missense_variant 0.4
eis 2714549 p.Met262Leu missense_variant 0.4
eis 2714561 p.Gly258Cys missense_variant 0.67
eis 2714764 p.Leu190Arg missense_variant 0.29
ahpC 2726522 p.Met110Ile missense_variant 0.29
folC 2746426 c.1173G>A synonymous_variant 0.5
folC 2747097 p.Val168Ile missense_variant 0.5
folC 2747137 c.462G>A synonymous_variant 1.0
folC 2747453 p.Arg49Gln missense_variant 1.0
pepQ 2859380 p.Gly347Arg missense_variant 1.0
pepQ 2859405 c.1014C>A synonymous_variant 0.33
pepQ 2859564 c.855C>T synonymous_variant 0.25
pepQ 2860220 p.Gln67* stop_gained 0.33
ribD 2987523 p.Thr229Ala missense_variant 1.0
Rv2752c 3064708 p.Arg495Leu missense_variant 1.0
Rv2752c 3065504 p.Asp230Asn missense_variant 0.4
thyA 3073977 c.495A>G synonymous_variant 0.5
ald 3087399 p.Val194Ile missense_variant 0.33
fbiD 3339239 p.Ala41Asp missense_variant 0.25
fbiD 3339290 p.Ser58Leu missense_variant 0.25
fbiD 3339742 p.Arg209* stop_gained 0.2
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449480 p.Glu326Gly missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474349 p.Pro115Thr missense_variant 0.29
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568512 c.168G>A synonymous_variant 0.33
whiB7 3568605 c.75C>A synonymous_variant 0.2
fbiA 3640407 c.-136G>A upstream_gene_variant 0.5
fbiA 3640834 p.Gln98* stop_gained 0.25
fbiA 3641441 p.Gly300Val missense_variant 1.0
alr 3840668 c.753G>A synonymous_variant 0.67
clpC1 4039601 c.1104G>A synonymous_variant 0.33
clpC1 4040315 c.390G>A synonymous_variant 0.25
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040526 p.Arg60His missense_variant 0.4
clpC1 4040668 p.Val13Ile missense_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241440 c.1578C>T synonymous_variant 0.29
embC 4241825 p.Pro655Thr missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243463 c.231G>A synonymous_variant 0.17
embA 4244249 c.1017C>T synonymous_variant 0.4
embA 4244456 c.1224C>G synonymous_variant 1.0
embA 4245687 p.Val819Phe missense_variant 0.4
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248563 p.Ala684Ser missense_variant 0.29
embB 4249049 p.Gly846Ser missense_variant 0.5
aftB 4268103 p.Ala245Val missense_variant 0.25
aftB 4268507 c.330G>A synonymous_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4328018 p.Arg157His missense_variant 1.0
whiB6 4338551 c.-30G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0