TB-Profiler result

Run: SRR7755687
Summary

Run ID: SRR7755687

Sample name:

Date: 04-04-2023 20:15:01

Number of reads: 1106437

Percentage reads mapped: 99.62

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 4327306 c.167delA frameshift_variant 0.11 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
gyrB 6021 p.Val261Glu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9301 p.Ala667Val missense_variant 0.18
fgd1 491762 p.Asp327Gly missense_variant 0.15
ccsA 620522 p.Ala211Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776355 p.Leu709Pro missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304033 p.Glu368Gly missense_variant 0.15
Rv1258c 1406266 p.Ala359Thr missense_variant 0.11
Rv1258c 1406513 c.827delT frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475086 n.1429C>T non_coding_transcript_exon_variant 0.12
inhA 1674952 p.Pro251Ala missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918532 p.Val198Ala missense_variant 0.17
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715490 c.-158A>G upstream_gene_variant 0.17
thyX 3067663 p.Arg95Cys missense_variant 0.15
whiB7 3568755 c.-76C>A upstream_gene_variant 0.25
alr 3841259 c.162G>A synonymous_variant 0.11
panD 4044402 c.-121T>C upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249354 c.2841G>C synonymous_variant 1.0
aftB 4268599 p.Glu80* stop_gained 0.11
aftB 4268751 p.Asp29Ala missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>C upstream_gene_variant 1.0
gid 4408334 c.-132G>A upstream_gene_variant 0.11
gid 4408376 c.-174A>T upstream_gene_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0