TB-Profiler result

Run: SRR6981998
Summary

Run ID: SRR6981998

Sample name:

Date: 04-04-2023 18:24:15

Number of reads: 387989

Percentage reads mapped: 99.7

Strain: lineage4.8.1;lineage4.4.1.1

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.17
lineage4.4 Euro-American S;T None 0.78
lineage4.4.1 Euro-American (S-type) S;T None 0.81
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.16
lineage4.4.1.1 Euro-American S;Orphans None 0.75
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 0.88
gyrA 9138 p.Gln613Glu missense_variant 0.86
gyrA 9304 p.Gly668Asp missense_variant 0.57
fgd1 491374 p.Lys198Glu missense_variant 0.14
ccsA 619779 c.-112A>G upstream_gene_variant 0.15
ccsA 620383 p.Pro165Ala missense_variant 0.17
ccsA 620463 c.573C>T synonymous_variant 0.6
rpoB 763203 p.Ser1133Thr missense_variant 0.13
rpoC 764725 p.Phe452Leu missense_variant 0.11
rpoC 766937 p.Asn1190Asp missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 0.44
mmpL5 777750 p.Arg244Leu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.21
rrl 1474039 n.382A>G non_coding_transcript_exon_variant 0.11
inhA 1674162 c.-40C>A upstream_gene_variant 0.17
inhA 1674728 p.Ala176Gly missense_variant 0.15
rpsA 1834754 p.Glu405Gln missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101882 c.1161C>T synonymous_variant 0.12
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168228 c.2385C>A synonymous_variant 0.17
PPE35 2168466 c.2145_2146delCC frameshift_variant 0.29
PPE35 2168479 p.Thr712Pro missense_variant 0.62
PPE35 2169840 p.Gly258Asp missense_variant 0.62
PPE35 2170506 p.Thr36Asn missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518519 c.405G>T synonymous_variant 0.12
eis 2714972 p.Ser121Arg missense_variant 0.12
pepQ 2859491 p.Val310Ile missense_variant 0.11
pepQ 2860496 c.-78C>A upstream_gene_variant 0.12
Rv2752c 3066281 c.-90A>G upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.76
fbiD 3339040 c.-78T>C upstream_gene_variant 0.35
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.59
whiB7 3568779 c.-100T>C upstream_gene_variant 0.92
Rv3236c 3612665 p.Val151Ala missense_variant 0.86
fbiB 3641019 c.-516G>T upstream_gene_variant 0.14
fbiB 3642874 p.Leu447Arg missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242748 c.-485A>C upstream_gene_variant 0.12
aftB 4267183 p.Gly552Arg missense_variant 0.13
ethA 4327323 p.Pro51Thr missense_variant 0.12
ethR 4327750 p.Lys68Glu missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338700 c.-179T>C upstream_gene_variant 0.12