TB-Profiler result

Run: SRR13837684
Summary

Run ID: SRR13837684

Sample name:

Date: 03-04-2023 09:15:51

Number of reads: 296593

Percentage reads mapped: 97.91

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 None 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 5192 c.-48C>G upstream_gene_variant 1.0
gyrB 6136 c.897G>A synonymous_variant 0.12
gyrB 6148 c.909C>G synonymous_variant 0.11
gyrB 6169 c.930C>G synonymous_variant 0.12
gyrB 6190 c.951A>G synonymous_variant 0.12
gyrB 6209 c.970C>T synonymous_variant 0.12
gyrB 6214 c.975G>C synonymous_variant 0.12
gyrB 6217 c.978G>C synonymous_variant 0.13
gyrB 6223 c.984G>C synonymous_variant 0.19
gyrB 6242 p.Arg335Lys missense_variant 0.15
gyrB 6250 c.1011A>G synonymous_variant 0.17
gyrB 6253 c.1014G>C synonymous_variant 0.17
gyrB 6280 c.1041T>C synonymous_variant 0.18
gyrB 6286 c.1047T>C synonymous_variant 0.18
gyrB 6292 c.1053G>C synonymous_variant 0.18
gyrB 6295 c.1056A>G synonymous_variant 0.2
gyrB 6298 c.1059C>T synonymous_variant 0.2
gyrB 6299 c.1060C>T synonymous_variant 0.2
gyrA 6307 c.-995T>G upstream_gene_variant 0.2
gyrA 6319 c.-983G>C upstream_gene_variant 0.22
gyrA 6325 c.-977C>G upstream_gene_variant 0.25
gyrA 6361 c.-941G>A upstream_gene_variant 0.29
gyrA 6362 c.-940T>C upstream_gene_variant 0.29
gyrA 9658 c.2357_2358insT frameshift_variant 1.0
fgd1 490779 c.-4A>T upstream_gene_variant 1.0
mshA 575713 c.366G>A synonymous_variant 0.13
mshA 575719 c.372C>T synonymous_variant 0.14
mshA 575734 c.387T>G synonymous_variant 0.14
mshA 575737 c.390T>C synonymous_variant 0.2
mshA 575746 c.399C>G synonymous_variant 0.2
mshA 575752 c.405G>A synonymous_variant 0.12
mshA 575767 c.420G>A synonymous_variant 0.15
mshA 575771 p.Val142Ser missense_variant 0.14
mshA 575779 c.432A>G synonymous_variant 0.14
mshA 575821 c.474G>C synonymous_variant 0.12
rpoB 760041 p.Gly79Arg missense_variant 1.0
rpoB 760652 c.846C>A synonymous_variant 0.92
rpoB 761122 p.Pro439Arg missense_variant 1.0
rpoC 764830 c.1461C>G synonymous_variant 0.22
mmpL5 775929 p.Asn851Ile missense_variant 1.0
mmpS5 778941 c.-36A>G upstream_gene_variant 1.0
rplC 801324 c.516T>C synonymous_variant 0.15
fbiC 1303584 c.654C>G synonymous_variant 0.29
fbiC 1303590 c.660A>G synonymous_variant 0.33
fbiC 1303602 c.672A>G synonymous_variant 0.33
fbiC 1303605 c.675C>G synonymous_variant 0.33
fbiC 1303608 c.678G>A synonymous_variant 0.33
fbiC 1303611 c.681G>C synonymous_variant 0.33
fbiC 1303614 c.684C>T synonymous_variant 0.33
fbiC 1303617 c.687C>G synonymous_variant 0.33
fbiC 1303632 c.702T>G synonymous_variant 0.33
fbiC 1303638 c.708A>G synonymous_variant 0.33
fbiC 1303653 c.723G>C synonymous_variant 0.33
fbiC 1303659 c.729T>C synonymous_variant 0.33
fbiC 1303660 p.Val244Thr missense_variant 0.33
fbiC 1303674 c.744C>G synonymous_variant 0.33
fbiC 1303686 c.756C>G synonymous_variant 0.33
fbiC 1303695 c.765T>C synonymous_variant 0.43
fbiC 1303708 c.778T>C synonymous_variant 0.29
fbiC 1303728 c.798G>A synonymous_variant 0.33
fbiC 1303836 c.906G>C synonymous_variant 0.18
embR 1417376 c.-29T>C upstream_gene_variant 1.0
rrl 1473740 n.83G>A non_coding_transcript_exon_variant 1.0
rrl 1474574 n.917A>T non_coding_transcript_exon_variant 1.0
rpsA 1834610 p.Arg357Gly missense_variant 1.0
ndh 2101828 c.1215C>T synonymous_variant 1.0
PPE35 2168706 p.Ser636Phe missense_variant 1.0
pncA 2289887 c.-646A>C upstream_gene_variant 1.0
folC 2746838 p.Ala254Glu missense_variant 1.0
ribD 2987500 p.Gly221Asp missense_variant 1.0
thyX 3068082 c.-137T>C upstream_gene_variant 1.0
fbiD 3338954 c.-164A>G upstream_gene_variant 1.0
fbiD 3339235 p.Leu40Val missense_variant 1.0
fbiD 3339406 p.Thr97Ala missense_variant 1.0
Rv3083 3448625 p.Leu41Gln missense_variant 1.0
fbiB 3642247 p.Asn238Thr missense_variant 1.0
fbiB 3642283 p.Glu250Ala missense_variant 1.0
rpoA 3877839 c.669G>C synonymous_variant 0.11
rpoA 3877857 c.651G>A synonymous_variant 0.11
rpoA 3877872 c.636C>T synonymous_variant 0.12
clpC1 4038530 p.Glu725Asp missense_variant 0.14
clpC1 4038536 c.2169C>T synonymous_variant 0.14
clpC1 4039483 c.1221_1222insC frameshift_variant 1.0
embA 4243843 c.613dupG frameshift_variant 1.0
embA 4244833 p.Val534Ala missense_variant 1.0
embA 4245735 p.Ala835Ser missense_variant 1.0
aftB 4267994 p.Met281Ile missense_variant 1.0