TB-Profiler result

Run: SRR3675531
Summary

Run ID: SRR3675531

Sample name:

Date: 04-04-2023 05:32:31

Number of reads: 500497

Percentage reads mapped: 98.38

Strain: lineage4.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.99
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 490896 p.Ser38Arg missense_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 762184 p.Gly793Val missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766288 c.2919C>A synonymous_variant 0.18
rpoC 766437 p.Asp1023Gly missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777935 c.546C>A synonymous_variant 0.18
mmpS5 778677 p.Lys77Glu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800788 c.-21A>T upstream_gene_variant 0.2
rplC 800981 p.Ser58Ile missense_variant 0.18
rplC 801187 p.Met127Val missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673155 c.-285G>C upstream_gene_variant 0.11
rpsA 1834236 p.Asp232Gly missense_variant 0.18
rpsA 1834387 c.846C>T synonymous_variant 0.33
rpsA 1834395 p.Arg285Gln missense_variant 0.29
rpsA 1834397 p.His286Thr missense_variant 0.29
rpsA 1834405 c.864C>G synonymous_variant 0.25
rpsA 1834409 p.Thr290Leu missense_variant 0.25
rpsA 1834415 p.Ala292Gln missense_variant 0.25
rpsA 1834423 c.882G>T synonymous_variant 0.25
rpsA 1834435 c.894G>C synonymous_variant 0.29
rpsA 1834451 c.910T>C synonymous_variant 0.4
rpsA 1834468 c.927A>G synonymous_variant 0.33
rpsA 1834477 c.936C>T synonymous_variant 0.33
rpsA 1834482 p.Glu314Gly missense_variant 0.33
rpsA 1834486 p.Glu315Asp missense_variant 0.33
rpsA 1834489 c.948T>C synonymous_variant 0.33
rpsA 1834495 c.954G>A synonymous_variant 0.33
rpsA 1834508 p.Ile323Val missense_variant 0.33
rpsA 1834804 c.1263C>T synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154612 c.1500G>A synonymous_variant 0.25
PPE35 2167792 p.Ser941Ala missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.63
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714179 p.Arg385Gln missense_variant 0.14
eis 2715083 p.Phe84Ile missense_variant 0.17
folC 2746443 p.Asp386Asn missense_variant 0.25
ribD 2986872 p.Thr12Ala missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087504 p.Val229Ile missense_variant 0.11
fbiD 3339692 p.Pro192His missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840362 c.1059G>A synonymous_variant 0.14
alr 3841369 c.51delG frameshift_variant 0.13
rpoA 3878059 p.Val150Ala missense_variant 0.15
clpC1 4040662 p.Leu15Met missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.21
embB 4246567 c.54G>T synonymous_variant 0.21
embB 4248394 c.1881G>T synonymous_variant 0.13
aftB 4267026 p.Arg604Leu missense_variant 0.22
ethA 4326185 p.Pro430His missense_variant 0.14
ethA 4328046 c.-573C>A upstream_gene_variant 0.29
whiB6 4338292 p.Ala77Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408298 c.-96A>G upstream_gene_variant 0.22