TB-Profiler result

Run: SRR21677875
Summary

Run ID: SRR21677875

Sample name:

Date: 04-04-2023 02:49:17

Number of reads: 578823

Percentage reads mapped: 99.15

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8864 c.1563C>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491410 p.Ala210Ser missense_variant 0.17
mshA 576749 p.Lys468Glu missense_variant 0.11
rpoB 761799 c.1993C>A synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778029 p.Val151Ala missense_variant 0.11
mmpL5 778042 p.Ala147Thr missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407024 p.Leu106Arg missense_variant 0.17
Rv1258c 1407293 c.38_47delTGTTCGCAAC frameshift_variant 0.11
Rv1258c 1407363 c.-23C>A upstream_gene_variant 0.14
embR 1416913 p.Trp145Cys missense_variant 0.15
embR 1417358 c.-11G>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.15
inhA 1674636 c.435C>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168150 c.2463T>C synonymous_variant 0.11
PPE35 2168206 p.Pro803Ala missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518141 c.27C>G synonymous_variant 0.12
kasA 2518336 c.222A>T synonymous_variant 0.22
kasA 2518919 p.Gly269Ser missense_variant 1.0
pepQ 2860568 c.-150C>T upstream_gene_variant 0.11
ribD 2986915 p.Gly26Asp missense_variant 0.12
ribD 2987432 p.Leu198Phe missense_variant 0.12
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073896 c.576C>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449248 p.Ala249Ser missense_variant 0.22
Rv3083 3449652 c.1149T>C synonymous_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612247 p.Met290Ile missense_variant 0.11
fbiA 3640729 p.Asp63Tyr missense_variant 0.11
rpoA 3878639 c.-132C>G upstream_gene_variant 0.4
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038392 c.2313C>A synonymous_variant 0.12
clpC1 4039198 p.Glu503* stop_gained 0.12
panD 4044054 c.227delC frameshift_variant 0.17
panD 4044417 c.-136C>G upstream_gene_variant 0.11
embC 4239962 p.Val34Leu missense_variant 0.14
embC 4241002 c.1140G>A synonymous_variant 0.12
embC 4241246 p.Arg462Trp missense_variant 0.13
embC 4242117 p.Ala752Val missense_variant 0.14
embC 4242563 p.Ala901Thr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.1
embB 4245653 c.-861C>A upstream_gene_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.16
embB 4246555 c.42G>C synonymous_variant 0.16
embB 4246556 p.Ala15Pro missense_variant 0.16
embB 4246563 p.Leu17Trp missense_variant 0.16
embB 4246567 c.54G>T synonymous_variant 0.16
embB 4247050 c.537C>T synonymous_variant 0.13
embB 4249024 c.2511C>T synonymous_variant 0.12
embB 4249632 p.Thr1040Asn missense_variant 0.25
aftB 4267590 p.Gln416Pro missense_variant 0.11
ubiA 4269878 c.-45A>C upstream_gene_variant 0.11
ubiA 4269887 c.-55delC upstream_gene_variant 0.11
ethR 4326799 c.-750G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0