TB-Profiler result

Run: SRR4035788
Summary

Run ID: SRR4035788

Sample name:

Date: 04-04-2023 07:17:55

Number of reads: 918732

Percentage reads mapped: 99.51

Strain: lineage4.1.2

Drug-resistance: Other

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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
lineage4.1.2 Euro-American T;H 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
pncA 2288982 c.259delA frameshift_variant 0.18 pyrazinamide, pyrazinamide
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 5496 p.Val86Asp missense_variant 0.22
gyrB 6369 p.Asn377Ile missense_variant 0.14
gyrA 6550 c.-752A>T upstream_gene_variant 0.2
gyrB 7164 p.Ala642Gly missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7590 p.Val97Leu missense_variant 0.17
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9249 p.Ala650Ser missense_variant 0.22
gyrA 9260 c.1959G>A synonymous_variant 0.17
gyrA 9265 p.Asp655Val missense_variant 0.17
gyrA 9274 p.Glu658Ala missense_variant 0.17
gyrA 9282 p.Gly661Arg missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9450 p.Val717Met missense_variant 0.17
fgd1 490881 c.99C>T synonymous_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575262 c.-86G>A upstream_gene_variant 0.14
mshA 576248 p.Pro301Ala missense_variant 0.15
mshA 576287 c.940C>A synonymous_variant 0.15
mshA 576341 p.Ser332Thr missense_variant 0.14
ccsA 619772 c.-119A>T upstream_gene_variant 0.22
ccsA 620546 c.660delC frameshift_variant 0.15
rpoB 759870 p.Ser22Pro missense_variant 0.13
rpoB 759980 c.174G>A synonymous_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760123 p.Phe106Ser missense_variant 0.12
rpoB 760915 p.Arg370His missense_variant 0.14
rpoB 760933 p.Gly376Ala missense_variant 0.14
rpoB 761058 p.Val418Leu missense_variant 0.11
rpoB 761094 p.Leu430Met missense_variant 0.13
rpoB 761650 p.Ser615Asn missense_variant 0.2
rpoB 762268 p.Glu821Ala missense_variant 0.12
rpoB 762606 p.Ala934Thr missense_variant 0.15
rpoB 762619 p.Trp938* stop_gained 0.14
rpoC 763338 c.-32A>T upstream_gene_variant 0.18
rpoC 764195 p.Ser276Pro missense_variant 0.13
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766324 c.2955C>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775787 c.2694C>T synonymous_variant 0.33
mmpL5 776366 c.2115G>A synonymous_variant 0.15
mmpL5 776886 p.Asn532Ile missense_variant 0.18
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpS5 778829 p.Gln26Arg missense_variant 0.12
mmpR5 779168 p.Leu60Pro missense_variant 0.12
mmpR5 779182 p.Gly65Trp missense_variant 0.14
mmpS5 779525 c.-620T>C upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800927 p.Arg40Leu missense_variant 0.12
fbiC 1303584 c.654C>A synonymous_variant 0.12
fbiC 1303594 p.Leu222Val missense_variant 0.12
fbiC 1304035 p.Arg369Trp missense_variant 0.2
embR 1416501 p.Ala283Thr missense_variant 0.17
embR 1416689 p.Arg220Pro missense_variant 0.15
embR 1416941 p.Arg136Pro missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471900 n.56delA non_coding_transcript_exon_variant 0.13
rrs 1471903 n.58A>T non_coding_transcript_exon_variant 0.12
rrs 1472792 n.947G>T non_coding_transcript_exon_variant 0.22
rrl 1474268 n.611C>T non_coding_transcript_exon_variant 0.25
rrl 1474457 n.800C>T non_coding_transcript_exon_variant 1.0
rrl 1474484 n.828delA non_coding_transcript_exon_variant 0.33
rrl 1474531 n.874G>A non_coding_transcript_exon_variant 0.2
rrl 1476307 n.2650A>C non_coding_transcript_exon_variant 0.15
rrl 1476795 n.3138A>G splice_region_variant&non_coding_transcript_exon_variant 0.25
inhA 1673628 c.-574C>G upstream_gene_variant 0.15
inhA 1674744 p.Lys181Asn missense_variant 0.17
rpsA 1834898 p.Ser453Gly missense_variant 0.17
tlyA 1917829 c.-111C>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103137 c.-95A>G upstream_gene_variant 0.12
ndh 2103163 c.-121A>G upstream_gene_variant 0.12
katG 2154094 p.Ala673Val missense_variant 0.22
katG 2155030 p.Ala361Val missense_variant 0.17
katG 2155847 p.Pro89Ser missense_variant 0.15
PPE35 2168370 p.Ala748Val missense_variant 0.2
PPE35 2169007 p.Ser536Pro missense_variant 0.11
PPE35 2170475 c.138C>T synonymous_variant 0.2
Rv1979c 2222451 c.714C>T synonymous_variant 0.25
Rv1979c 2222687 p.Lys160* stop_gained 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288714 c.528C>A synonymous_variant 0.13
pncA 2288835 p.Asp136Val missense_variant 0.18
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715347 c.-15C>T upstream_gene_variant 0.12
ahpC 2726049 c.-144A>T upstream_gene_variant 0.13
folC 2747326 c.273G>A synonymous_variant 0.18
pepQ 2859510 c.909T>C synonymous_variant 0.17
pepQ 2859616 p.Ala268Val missense_variant 0.13
pepQ 2860551 c.-133C>A upstream_gene_variant 0.13
thyX 3067413 p.Ala178Val missense_variant 0.17
thyA 3074065 p.Gly136Asp missense_variant 0.13
thyA 3074522 c.-51C>G upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338919 c.-199C>A upstream_gene_variant 0.13
Rv3083 3448634 p.Thr44Ser missense_variant 0.13
Rv3083 3449380 p.Trp293Arg missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474934 p.Arg310Cys missense_variant 0.14
fprA 3475034 p.Asn343Ser missense_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612139 c.978T>C synonymous_variant 0.2
Rv3236c 3612905 p.Leu71Ser missense_variant 0.25
Rv3236c 3612943 c.174C>A synonymous_variant 0.25
Rv3236c 3613085 p.Leu11Pro missense_variant 0.14
Rv3236c 3613119 c.-3C>G upstream_gene_variant 0.11
fbiB 3641543 c.9C>T synonymous_variant 0.15
fbiB 3642200 c.666G>C synonymous_variant 0.18
alr 3841386 p.Asn12Ser missense_variant 0.14
clpC1 4038173 c.2532G>A synonymous_variant 0.12
clpC1 4038388 c.2317T>C synonymous_variant 0.11
clpC1 4039070 c.1635G>A synonymous_variant 0.15
clpC1 4039108 p.Arg533Gly missense_variant 0.12
clpC1 4039169 c.1536A>G synonymous_variant 0.12
clpC1 4039196 c.1509G>A synonymous_variant 0.17
clpC1 4039205 c.1500C>T synonymous_variant 0.18
clpC1 4039909 p.Glu266* stop_gained 0.29
clpC1 4040492 c.213G>A synonymous_variant 0.12
embC 4239757 c.-106G>A upstream_gene_variant 0.2
embC 4240418 p.Gly186Ser missense_variant 0.17
embC 4241133 p.Pro424Leu missense_variant 0.15
embC 4241836 c.1974A>G synonymous_variant 0.21
embC 4242197 p.Ala779Thr missense_variant 0.2
embA 4242322 c.-911C>A upstream_gene_variant 0.14
embC 4242326 p.Thr822Ala missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4242973 c.-260G>A upstream_gene_variant 0.17
embC 4242993 p.Thr1044Met missense_variant 0.14
embA 4243838 c.606C>T synonymous_variant 0.12
aftB 4267811 c.1026G>A synonymous_variant 0.25
aftB 4268174 c.663G>A synonymous_variant 0.25
aftB 4268182 p.Phe219Leu missense_variant 0.25
aftB 4268587 c.250T>C synonymous_variant 0.11
aftB 4268770 p.Gln23* stop_gained 0.13
ethA 4326202 c.1272A>G synonymous_variant 0.13
ethA 4326899 p.Pro192Leu missense_variant 0.15
ethA 4327488 c.-15T>C upstream_gene_variant 0.2
ethA 4327821 c.-348G>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0