TB-Profiler result

Run: SRR13837566
Summary

Run ID: SRR13837566

Sample name:

Date: 03-04-2023 09:13:25

Number of reads: 595276

Percentage reads mapped: 97.25

Strain: lineage4.9

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
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
ethA 4326568 c.905delT frameshift_variant 1.0 ethionamide
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 8820 p.Asp507His missense_variant 1.0
mshA 575967 p.Val207Asp missense_variant 1.0
rpoB 759961 p.Thr52Asn missense_variant 1.0
rpoB 763050 p.Leu1082Met missense_variant 1.0
rpoC 763801 c.432C>G synonymous_variant 0.18
rpoC 763807 c.438T>C synonymous_variant 0.15
rpoC 763819 c.450G>C synonymous_variant 0.19
rpoC 763831 c.462A>G synonymous_variant 0.13
rpoC 763835 p.Ala156Met missense_variant 0.13
rpoC 763858 c.489A>G synonymous_variant 0.13
rpoC 763876 p.Glu169Asp missense_variant 0.13
rpoC 763879 c.510A>G synonymous_variant 0.13
rpoC 763888 c.519G>C synonymous_variant 0.13
rpoC 763891 c.522G>C synonymous_variant 0.13
rpoC 763894 c.525A>G synonymous_variant 0.13
rpoC 763919 c.550C>T synonymous_variant 0.12
rpoC 763933 c.564C>T synonymous_variant 0.11
rpoC 763945 c.576T>C synonymous_variant 0.16
rpoC 764059 c.690G>C synonymous_variant 0.14
rpoC 767134 c.3765C>G synonymous_variant 0.12
mmpL5 775701 p.Pro927Gln missense_variant 1.0
mmpL5 778828 c.-348G>A upstream_gene_variant 1.0
rplC 801353 p.Val182Ala missense_variant 1.0
fbiC 1304512 p.Val528Ile missense_variant 1.0
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.12
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.12
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.17
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.14
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.13
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.14
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.13
fabG1 1673633 p.Ser65Asn missense_variant 0.12
rpsA 1834175 p.Arg212* stop_gained 1.0
Rv1979c 2222085 c.1080G>C synonymous_variant 1.0
folC 2746135 c.1464A>C stop_lost&splice_region_variant 1.0
folC 2747317 c.282C>G synonymous_variant 0.12
folC 2747355 p.Val82Ile missense_variant 0.13
folC 2747359 c.240C>G synonymous_variant 0.13
folC 2747362 c.237G>C synonymous_variant 0.13
folC 2747394 p.Ile69Val missense_variant 0.12
folC 2747395 c.204T>C synonymous_variant 0.12
folC 2747401 c.198G>C synonymous_variant 0.12
folC 2747407 c.192T>C synonymous_variant 0.12
folC 2747419 c.180C>G synonymous_variant 0.12
thyA 3073839 c.633T>C synonymous_variant 0.11
thyA 3073872 p.Ile200Val missense_variant 0.16
thyA 3073878 c.594G>A synonymous_variant 0.17
thyA 3073892 c.580T>C synonymous_variant 0.2
thyA 3073893 c.579C>G synonymous_variant 0.2
thyA 3073925 c.547T>C synonymous_variant 0.15
thyA 3073926 c.546G>C synonymous_variant 0.14
thyA 3073929 c.543T>C synonymous_variant 0.14
thyA 3073953 c.519T>C synonymous_variant 0.13
ald 3087218 p.Met133Ile missense_variant 0.94
whiB7 3568679 p.Val1Leu missense_variant 1.0
rpoA 3877782 c.726T>C synonymous_variant 0.12
rpoA 3878292 c.216T>C synonymous_variant 0.11
clpC1 4039409 c.1296T>C synonymous_variant 0.12
clpC1 4039412 c.1293T>G synonymous_variant 0.12
clpC1 4039430 c.1275T>C synonymous_variant 0.17
clpC1 4039442 c.1263A>G synonymous_variant 0.14
clpC1 4039448 c.1257A>G synonymous_variant 0.13
clpC1 4039454 c.1251A>G synonymous_variant 0.12
clpC1 4039463 c.1242C>G synonymous_variant 0.12
clpC1 4039466 c.1239T>C synonymous_variant 0.13
clpC1 4039469 c.1236T>C synonymous_variant 0.12
clpC1 4039481 c.1224T>G synonymous_variant 0.13
clpC1 4039484 c.1221T>G synonymous_variant 0.13
clpC1 4040066 c.639G>T synonymous_variant 1.0
embC 4241259 c.1397_1398insT frameshift_variant 1.0
embA 4243358 c.126C>T synonymous_variant 1.0
embA 4243469 c.237C>T synonymous_variant 1.0
embB 4248436 c.1923C>T synonymous_variant 0.91
ubiA 4269557 p.Ala93Pro missense_variant 1.0