TB-Profiler result

Run: SRR2101409
Summary

Run ID: SRR2101409

Sample name:

Date: 03-04-2023 23:41:56

Number of reads: 501660

Percentage reads mapped: 99.78

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.98
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 6009 p.Leu257Pro missense_variant 0.12
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 6869 c.-433T>C upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9790 p.Ala830Gly missense_variant 0.11
fgd1 490936 p.Pro52Thr missense_variant 0.12
fgd1 491054 p.Ala91Val missense_variant 0.12
mshA 576466 c.1119G>T synonymous_variant 0.13
ccsA 619784 c.-107G>T upstream_gene_variant 0.14
ccsA 619831 c.-60T>G upstream_gene_variant 0.3
ccsA 620505 c.615G>A synonymous_variant 0.15
rpoB 760630 p.Leu275Pro missense_variant 0.11
rpoB 760748 c.942C>T synonymous_variant 0.14
rpoB 761537 c.1731C>A synonymous_variant 0.12
rpoB 762384 p.Asn860Asp missense_variant 0.11
rpoC 763463 p.Glu32* stop_gained 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766401 p.Thr1011Ile missense_variant 0.1
rpoC 766859 c.3490C>A synonymous_variant 0.11
rpoC 766925 p.Phe1186Leu missense_variant 0.1
rpoC 767088 p.Cys1240Phe missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305051 c.2121G>T synonymous_variant 0.12
embR 1417063 c.285C>A synonymous_variant 0.13
embR 1417137 p.Ser71Gly missense_variant 0.13
embR 1417381 c.-34G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472115 n.270C>T non_coding_transcript_exon_variant 0.22
rrs 1472116 n.271C>T non_coding_transcript_exon_variant 0.22
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.18
rrl 1476708 n.3051C>A non_coding_transcript_exon_variant 0.29
rrl 1476728 n.3071T>A non_coding_transcript_exon_variant 0.29
inhA 1674779 p.Pro193His missense_variant 0.14
rpsA 1834205 p.Phe222Leu missense_variant 0.15
rpsA 1834467 p.Ala309Glu missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918066 p.Ala43Pro missense_variant 0.22
ndh 2103230 c.-189delG upstream_gene_variant 0.18
PPE35 2169120 p.Val498Gly missense_variant 0.13
PPE35 2170011 p.Arg201Gln missense_variant 0.18
PPE35 2170150 p.His155Asn missense_variant 0.17
Rv1979c 2222444 p.Ala241Thr missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289232 c.10T>C synonymous_variant 0.13
eis 2714926 p.Thr136Ser missense_variant 1.0
eis 2714986 p.Ala116Val missense_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.21
ribD 2986641 c.-198G>T upstream_gene_variant 0.17
Rv2752c 3067116 c.-925C>A upstream_gene_variant 0.13
thyX 3068104 c.-159C>T upstream_gene_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087898 p.Gly360Val missense_variant 0.11
fbiD 3339279 c.162T>G synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474791 p.Pro262Gln missense_variant 0.12
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612122 p.Ala332Val missense_variant 0.12
fbiA 3641099 c.561delT frameshift_variant 0.17
fbiB 3642755 c.1221G>A synonymous_variant 0.13
alr 3840469 p.Val318Met missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840965 c.456G>A synonymous_variant 0.2
alr 3841264 p.Arg53Cys missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 0.92
panD 4044324 c.-43C>A upstream_gene_variant 0.25
embC 4239998 p.Ala46Ser missense_variant 0.29
embC 4240675 c.813C>T synonymous_variant 0.14
embC 4241008 c.1146G>C synonymous_variant 0.15
embC 4241879 p.Leu673Met missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242665 p.Ala935Thr missense_variant 0.13
embA 4243542 p.Gly104Arg missense_variant 0.11
embB 4247226 p.Arg238His missense_variant 0.12
embB 4248685 c.2172C>A synonymous_variant 0.14
embB 4249453 c.2940G>A synonymous_variant 0.18
aftB 4268510 p.Ser109Arg missense_variant 0.12
whiB6 4338537 c.-16T>C upstream_gene_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0