TB-Profiler result

Run: SRR4035758

Summary

Run ID: SRR4035758

Sample name:

Date: 04-04-2023 07:16:48

Number of reads: 1188552

Percentage reads mapped: 99.45

Strain: lineage4.1.2

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
lineage4.1.2 Euro-American T;H None 0.99
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 5393 p.Asn52Asp missense_variant 0.11
gyrB 6927 p.Leu563Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7637 c.336C>A synonymous_variant 0.13
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8599 p.Gln433Arg missense_variant 0.12
gyrA 8907 p.Ser536Gly missense_variant 0.11
gyrA 9188 p.Asn629Lys missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491048 p.Ala89Val missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575690 p.Gly115Arg missense_variant 0.13
mshA 576082 c.735C>T synonymous_variant 0.15
mshA 576117 p.Ala257Val missense_variant 0.29
mshA 576124 c.777A>T synonymous_variant 0.29
ccsA 620186 p.Gly99Asp missense_variant 0.25
ccsA 620429 p.Ser180Asn missense_variant 0.25
ccsA 620782 p.Ala298Thr missense_variant 0.18
ccsA 620794 p.Ala302Thr missense_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761000 p.Met398Ile missense_variant 0.17
rpoB 761475 p.Arg557Cys missense_variant 0.15
rpoB 761800 p.Arg665Pro missense_variant 0.12
rpoB 762387 c.2582delA frameshift_variant 0.11
rpoB 762595 c.2792delG frameshift_variant 0.22
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764983 c.1614T>C synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767086 c.3717C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776238 p.Gly748Ala missense_variant 0.12
mmpL5 776280 p.Arg734His missense_variant 0.13
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 778311 p.Gly57Val missense_variant 0.13
mmpL5 778449 p.Gly11Asp missense_variant 0.13
mmpS5 778801 p.Glu35Asp missense_variant 0.14
mmpR5 779336 c.349delC frameshift_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781528 c.-32A>G upstream_gene_variant 0.12
rplC 800914 p.Val36Ile missense_variant 0.12
rplC 801167 p.Gly120Asp missense_variant 0.17
rplC 801428 p.Met207Thr missense_variant 0.11
fbiC 1304701 p.Ala591Pro missense_variant 0.11
fbiC 1304978 p.Gly683Asp missense_variant 0.13
Rv1258c 1406899 p.Ala148Pro missense_variant 0.15
embR 1417359 c.-12G>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472576 n.734delG non_coding_transcript_exon_variant 0.13
rrs 1473190 n.1345G>A non_coding_transcript_exon_variant 0.13
rrl 1473432 n.-226G>T upstream_gene_variant 0.12
rrl 1473740 n.83G>C non_coding_transcript_exon_variant 0.11
rrl 1476064 n.2407A>G non_coding_transcript_exon_variant 0.13
inhA 1674421 c.220T>C synonymous_variant 0.15
inhA 1674500 p.Gln100Leu missense_variant 0.17
inhA 1674506 p.Gly102Ala missense_variant 0.18
tlyA 1917791 c.-149C>T upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918079 p.Ser47Phe missense_variant 0.12
tlyA 1918684 p.Arg249Gly missense_variant 0.11
ndh 2102331 p.Lys238Glu missense_variant 0.11
ndh 2102461 p.Glu194Asp missense_variant 0.13
ndh 2102805 p.Arg80Gly missense_variant 0.15
ndh 2103190 c.-149delG upstream_gene_variant 0.15
ndh 2103213 c.-171G>T upstream_gene_variant 0.14
PPE35 2170327 p.Glu96Lys missense_variant 0.17
PPE35 2170380 p.Ala78Glu missense_variant 0.2
PPE35 2170744 c.-132T>C upstream_gene_variant 0.1
Rv1979c 2222106 c.1058delT frameshift_variant 0.13
Rv1979c 2222903 c.261delG frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289080 c.162G>T synonymous_variant 0.12
pncA 2289636 c.-395A>G upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518995 p.Ser294Leu missense_variant 0.13
eis 2714223 c.1110C>A synonymous_variant 0.13
folC 2746918 c.681G>A synonymous_variant 0.13
pepQ 2859601 c.817delG frameshift_variant 0.15
pepQ 2859955 p.Thr155Ile missense_variant 0.2
pepQ 2860338 c.81G>A synonymous_variant 0.13
ribD 2986709 c.-130C>T upstream_gene_variant 0.12
ribD 2987333 p.Cys165Trp missense_variant 0.13
ribD 2987503 p.Gly222Val missense_variant 0.14
Rv2752c 3065372 p.Arg274Gly missense_variant 0.12
Rv2752c 3065665 p.Leu176* stop_gained 0.13
Rv2752c 3065763 p.Tyr143* stop_gained 0.25
Rv2752c 3066064 p.Ile43Asn missense_variant 0.12
thyX 3067475 c.471A>G synonymous_variant 0.12
thyA 3074033 p.His147Tyr missense_variant 0.18
thyA 3074543 c.-72T>C upstream_gene_variant 0.12
ald 3086763 c.-57T>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339183 c.70delA frameshift_variant 0.2
fbiD 3339531 c.414C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568465 p.Asp72Gly missense_variant 0.14
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612326 p.Thr264Ser missense_variant 0.12
fbiA 3641254 p.Ala238Thr missense_variant 0.18
alr 3841613 c.-193A>G upstream_gene_variant 0.11
rpoA 3877820 p.Glu230Gln missense_variant 0.12
rpoA 3877835 c.672delA frameshift_variant 0.14
rpoA 3877945 p.Asp188Val missense_variant 0.14
rpoA 3878645 c.-138G>T upstream_gene_variant 0.2
ddn 3986779 c.-65A>G upstream_gene_variant 0.13
clpC1 4038397 c.2304delG frameshift_variant 0.12
clpC1 4039119 c.1585delT frameshift_variant 0.13
panD 4044028 p.Val85Gly missense_variant 0.14
panD 4044356 c.-75T>C upstream_gene_variant 0.12
panD 4044458 c.-178delA upstream_gene_variant 0.13
embC 4239920 p.Arg20Cys missense_variant 0.14
embC 4242107 p.Cys749Arg missense_variant 0.15
embC 4242596 p.Gly912Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242929 p.Pro1023Ser missense_variant 0.13
embA 4243713 p.Thr161Ala missense_variant 0.11
embA 4244262 c.1030C>T synonymous_variant 0.12
embA 4245073 p.Leu614Pro missense_variant 0.14
embB 4247722 c.1209G>A synonymous_variant 0.12
embB 4248281 p.Thr590Ala missense_variant 0.1
embB 4248672 p.Ala720Gly missense_variant 0.11
embB 4248683 c.2172delC frameshift_variant 0.11
embB 4248702 p.Tyr730Cys missense_variant 0.1
aftB 4267324 p.Ile505Phe missense_variant 0.2
aftB 4268797 p.Ala14Thr missense_variant 0.2
aftB 4268868 c.-32G>C upstream_gene_variant 0.11
ubiA 4269787 p.Gly16Glu missense_variant 0.14
ubiA 4269979 c.-146T>C upstream_gene_variant 0.2
ubiA 4270023 c.-190G>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407744 p.Ile153Met missense_variant 0.17