TB-Profiler result

Run: SRR7645937

Summary

Run ID: SRR7645937

Sample name:

Date: 04-04-2023 19:59:22

Number of reads: 1109923

Percentage reads mapped: 99.63

Strain: lineage4.8

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 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 5097 c.-143A>C upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9258 p.Leu653Met missense_variant 0.17
gyrA 9285 p.Ala662Ser missense_variant 0.18
gyrA 9663 p.Ala788Thr missense_variant 0.12
mshA 576678 p.Ala444Val missense_variant 0.18
rpoB 759921 p.Arg39Cys missense_variant 0.13
rpoB 760790 c.984C>A synonymous_variant 0.25
rpoC 762650 c.-720C>T upstream_gene_variant 0.18
rpoB 762714 p.Val970Met missense_variant 0.15
rpoB 763099 c.3295delG frameshift_variant 0.14
rpoC 764765 p.Ala466Thr missense_variant 0.14
rpoC 766770 p.Leu1134Pro missense_variant 0.13
rpoC 767268 p.Ala1300Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776030 c.2451G>A synonymous_variant 0.12
mmpL5 776224 p.Gly753* stop_gained 0.14
mmpL5 777155 c.1326G>T synonymous_variant 0.18
mmpL5 777318 p.Arg388His missense_variant 0.17
mmpL5 777328 p.Ala385Thr missense_variant 0.17
mmpL5 779289 c.-809G>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304103 c.1175_1178delTGAC frameshift_variant 0.12
fbiC 1304109 c.1179C>T synonymous_variant 0.12
fbiC 1305388 p.Ala820Thr missense_variant 0.17
Rv1258c 1406123 p.Ala406Val missense_variant 0.13
Rv1258c 1407112 p.Val77Leu missense_variant 0.18
Rv1258c 1407525 c.-185C>T upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473317 n.1472G>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475016 n.1359C>T non_coding_transcript_exon_variant 0.2
rpsA 1834156 c.615C>T synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918626 c.687G>A synonymous_variant 0.15
tlyA 1918715 p.Ala259Val missense_variant 0.12
katG 2155827 c.285C>T synonymous_variant 0.15
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168247 p.Leu789Arg missense_variant 1.0
PPE35 2168542 p.Thr691Ala missense_variant 0.11
PPE35 2168871 p.Leu581Gln missense_variant 0.14
PPE35 2169395 c.1218C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289952 c.-711C>G upstream_gene_variant 1.0
pncA 2290153 c.-912C>T upstream_gene_variant 0.25
kasA 2519203 c.1089C>T synonymous_variant 0.17
folC 2747299 c.300C>T synonymous_variant 0.11
ald 3086667 c.-152delG upstream_gene_variant 0.12
ald 3087270 p.Arg151* stop_gained 0.22
Rv3236c 3613135 c.-19G>A upstream_gene_variant 0.13
fbiA 3641105 p.Val188Asp missense_variant 0.11
fbiA 3641491 p.Ala317Thr missense_variant 0.11
alr 3841189 p.Ala78Ser missense_variant 0.18
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.22
embC 4241196 p.Ser445* stop_gained 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243410 p.Ala60Ser missense_variant 0.25
embA 4244159 c.927G>T synonymous_variant 0.43
embA 4244381 c.1149G>A synonymous_variant 0.25
embA 4246020 p.Ala930Ser missense_variant 0.1
embB 4247890 c.1377C>T synonymous_variant 0.14
aftB 4267583 c.1254C>T synonymous_variant 0.2
ubiA 4269203 p.Glu211* stop_gained 0.13
ubiA 4269321 c.512delC frameshift_variant 0.2
ethA 4326296 p.Leu393Pro missense_variant 0.14
ethR 4327556 p.Thr3Asn missense_variant 0.11
ethA 4328266 c.-794delG upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0