TB-Profiler result

Run: SRR6855852
Summary

Run ID: SRR6855852

Sample name:

Date: 04-04-2023 17:47:51

Number of reads: 201517

Percentage reads mapped: 99.44

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
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 5575 p.Asp112Glu missense_variant 0.29
gyrB 5941 c.702T>C synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8997 c.1696T>C synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575662 c.315C>T synonymous_variant 0.14
ccsA 620262 c.372C>A synonymous_variant 0.29
ccsA 620604 c.714C>A synonymous_variant 0.33
rpoB 759674 c.-133T>C upstream_gene_variant 0.11
rpoC 763664 p.Ala99Ser missense_variant 0.17
rpoC 764815 p.Gln482His missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765764 p.Ile799Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778571 c.334delA frameshift_variant 0.13
mmpL5 778576 c.-96T>C upstream_gene_variant 0.13
mmpL5 779184 c.-704C>A upstream_gene_variant 0.14
mmpR5 779456 p.Arg156Gln missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302879 c.-52T>A upstream_gene_variant 0.2
embR 1417241 p.Arg36Gln missense_variant 0.29
embR 1417357 c.-10A>G upstream_gene_variant 0.12
embR 1417359 c.-12G>A upstream_gene_variant 0.12
rrs 1471648 n.-198A>G upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472031 n.186G>T non_coding_transcript_exon_variant 0.18
rrl 1473673 n.16G>T non_coding_transcript_exon_variant 0.18
rrl 1474084 n.431delA non_coding_transcript_exon_variant 0.33
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.13
rrl 1475952 n.2295A>T non_coding_transcript_exon_variant 0.18
rrl 1476493 n.2836A>G non_coding_transcript_exon_variant 0.15
fabG1 1673757 p.Glu106Asp missense_variant 0.22
inhA 1674868 p.Asp223Tyr missense_variant 0.14
rpsA 1834688 p.Ser383Gly missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167665 p.Gln983Arg missense_variant 0.18
PPE35 2168365 p.Thr750Ala missense_variant 0.33
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170239 p.Leu125Pro missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289106 p.Ala46Ser missense_variant 0.13
pncA 2289167 c.75C>G synonymous_variant 0.12
pncA 2289763 c.-523delT upstream_gene_variant 0.33
kasA 2518181 p.Thr23Ser missense_variant 0.18
eis 2714347 p.Phe329Tyr missense_variant 0.2
eis 2714563 p.Ile257Thr missense_variant 0.2
ribD 2986656 c.-183A>G upstream_gene_variant 0.12
Rv2752c 3065420 c.772C>A synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087343 p.Gly175Val missense_variant 0.22
Rv3083 3449778 c.1275T>C synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612872 p.Phe82Ser missense_variant 0.29
Rv3236c 3613143 c.-27A>G upstream_gene_variant 0.25
fbiA 3641447 p.Thr302Met missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3877969 p.Ala180Val missense_variant 0.2
rpoA 3877975 c.532delG frameshift_variant 0.2
ddn 3986772 c.-72T>C upstream_gene_variant 0.25
clpC1 4040158 p.Met183Leu missense_variant 0.18
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241954 p.Ala698Thr missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244073 p.Ala281Thr missense_variant 0.33
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249550 p.Arg1013Ser missense_variant 0.14
aftB 4268855 c.-19G>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408345 c.-143C>T upstream_gene_variant 0.15