TB-Profiler result

Run: ERR2229393

Summary

Run ID: ERR2229393

Sample name:

Date: 31-03-2023 17:09:59

Number of reads: 935119

Percentage reads mapped: 98.9

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
tlyA 1918211 p.Ala91Glu missense_variant 0.12 capreomycin
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 6013 c.774G>T synonymous_variant 0.18
gyrB 6364 p.Leu375Phe missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7395 p.Ala32Ser missense_variant 0.14
gyrA 7631 c.330G>T synonymous_variant 0.21
gyrA 7727 c.427delA frameshift_variant 0.11
gyrA 7899 p.Ala200Thr missense_variant 0.18
gyrA 7928 c.627C>T synonymous_variant 0.15
fgd1 491097 c.315G>A synonymous_variant 0.18
fgd1 491164 c.382C>A synonymous_variant 0.13
mshA 575709 p.Asp121Val missense_variant 0.15
mshA 576111 p.Ala255Gly missense_variant 0.22
rpoB 759743 c.-64G>A upstream_gene_variant 0.14
rpoB 759753 c.-54C>A upstream_gene_variant 0.17
rpoB 760412 c.606C>A synonymous_variant 0.22
rpoB 760621 p.Tyr272Cys missense_variant 0.14
rpoB 761284 p.Ser493* stop_gained 0.17
rpoB 761529 p.Val575Phe missense_variant 0.13
rpoC 762656 c.-714C>A upstream_gene_variant 0.2
rpoB 762675 p.Leu957Met missense_variant 0.18
rpoC 765158 p.Gly597Cys missense_variant 0.18
rpoC 765189 p.Pro607Leu missense_variant 0.13
rpoC 765215 p.Ala616Ser missense_variant 0.12
rpoC 766401 p.Thr1011Asn missense_variant 0.2
rpoC 767193 p.Thr1275Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775727 c.2754C>G synonymous_variant 0.15
mmpL5 775736 c.2745C>G synonymous_variant 0.14
mmpL5 775741 c.2740C>T synonymous_variant 0.13
mmpL5 775742 c.2739C>T synonymous_variant 0.13
mmpL5 775883 p.Ile866Met missense_variant 0.12
mmpL5 775981 p.Leu834Met missense_variant 0.13
mmpL5 775987 p.His832Tyr missense_variant 0.15
mmpL5 775990 c.2491C>T synonymous_variant 0.15
mmpL5 776530 p.Gln651Lys missense_variant 0.13
mmpL5 777133 p.Val450Phe missense_variant 0.12
mmpL5 777157 c.1324C>A synonymous_variant 0.17
mmpL5 777164 c.1317C>T synonymous_variant 0.18
mmpL5 777456 p.Gly342Val missense_variant 0.17
mmpL5 779397 c.-917C>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781504 c.-56G>T upstream_gene_variant 0.15
rplC 800856 c.48A>C synonymous_variant 0.17
rplC 801074 p.Ser89Leu missense_variant 0.15
fbiC 1303706 p.Leu259Pro missense_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304255 p.Ala442Glu missense_variant 0.2
fbiC 1304445 c.1515G>A synonymous_variant 0.25
Rv1258c 1406681 p.Trp220Cys missense_variant 0.18
embR 1416805 c.543A>G synonymous_variant 0.17
embR 1417140 p.Ala70Thr missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471983 n.138C>G non_coding_transcript_exon_variant 0.13
rrs 1472104 n.259G>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474763 n.1106G>T non_coding_transcript_exon_variant 0.15
rrl 1475312 n.1655C>A non_coding_transcript_exon_variant 0.14
rrl 1475732 n.2075T>A non_coding_transcript_exon_variant 0.15
rrl 1476486 n.2829C>T non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.43
inhA 1673730 c.-472C>A upstream_gene_variant 0.13
rpsA 1834129 c.588C>A synonymous_variant 0.17
rpsA 1834720 c.1179C>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102073 p.Ala324Ser missense_variant 0.14
ndh 2103143 c.-101G>T upstream_gene_variant 0.15
PPE35 2167745 c.2868C>G synonymous_variant 0.14
PPE35 2167814 c.2799C>T synonymous_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.19
PPE35 2167967 c.2646A>C synonymous_variant 0.19
PPE35 2167973 c.2640A>G synonymous_variant 0.27
PPE35 2168064 p.Thr850Ile missense_variant 0.12
PPE35 2168114 c.2499T>C synonymous_variant 0.12
PPE35 2168497 p.Ile706Val missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169101 c.1512G>T synonymous_variant 0.17
PPE35 2169875 c.738T>C synonymous_variant 0.12
PPE35 2169884 c.729T>C synonymous_variant 0.16
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.61
PPE35 2170053 p.Thr187Ser missense_variant 0.6
PPE35 2170147 p.Ser156Ala missense_variant 0.16
PPE35 2170372 p.Thr81Ala missense_variant 0.14
PPE35 2170535 c.78G>C synonymous_variant 0.18
PPE35 2170547 c.66A>C synonymous_variant 0.12
Rv1979c 2222795 p.Asp124Asn missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288709 p.Ala178Asp missense_variant 0.15
pncA 2289152 c.90C>T synonymous_variant 0.25
pncA 2289767 c.-526T>G upstream_gene_variant 0.15
kasA 2519281 c.1167G>T synonymous_variant 0.15
ahpC 2725996 c.-197A>G upstream_gene_variant 0.18
folC 2746753 c.846C>A synonymous_variant 0.4
folC 2746929 p.Pro224Thr missense_variant 0.29
folC 2747604 c.-6G>T upstream_gene_variant 0.33
pepQ 2859301 c.1118A>G stop_lost&splice_region_variant 0.18
pepQ 2859408 c.1011C>A synonymous_variant 0.12
pepQ 2860028 p.Leu131Met missense_variant 0.18
pepQ 2860511 c.-93C>A upstream_gene_variant 0.13
ribD 2987196 p.Val120Phe missense_variant 0.12
Rv2752c 3065923 p.Ile90Thr missense_variant 0.29
thyX 3067615 p.Glu111* stop_gained 0.15
thyA 3073989 p.Cys161* stop_gained 0.22
thyA 3074401 p.Thr24Asn missense_variant 0.18
thyA 3074490 c.-19G>A upstream_gene_variant 0.33
ald 3087663 p.Thr282Ala missense_variant 0.14
fprA 3474224 p.Asp73Ala missense_variant 0.22
fprA 3474706 p.Thr234Ala missense_variant 0.13
Rv3236c 3613041 c.76C>A synonymous_variant 0.25
fbiB 3642136 p.Ala201Asp missense_variant 0.3
alr 3840242 p.Ser393Arg missense_variant 0.14
alr 3840738 p.Arg228Leu missense_variant 0.14
rpoA 3877830 p.Asn226Lys missense_variant 0.18
rpoA 3878030 p.Gly160Arg missense_variant 0.22
ddn 3986922 p.Trp27Arg missense_variant 0.17
clpC1 4038303 p.Thr801Asn missense_variant 0.18
clpC1 4038989 c.1716T>C synonymous_variant 0.2
clpC1 4039106 c.1599G>A synonymous_variant 0.12
clpC1 4039691 c.1014G>C synonymous_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.31
panD 4044180 p.Asp34Glu missense_variant 0.18
embC 4239951 p.Arg30Gln missense_variant 0.18
embC 4240196 c.335delA frameshift_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242752 c.-481C>A upstream_gene_variant 0.17
embA 4243388 p.Asp52Glu missense_variant 0.18
embA 4243672 p.Gly147Val missense_variant 0.22
embA 4244132 c.900G>T synonymous_variant 0.13
embA 4244426 c.1194G>A synonymous_variant 0.29
embA 4244722 p.Gln497Arg missense_variant 0.11
embA 4244918 c.1686G>T synonymous_variant 0.17
embA 4245381 p.Thr717Ala missense_variant 0.22
embA 4245715 p.Leu828Pro missense_variant 0.15
embA 4245952 p.Pro907Leu missense_variant 0.25
embB 4246525 c.12C>T synonymous_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.56
embB 4246548 p.Pro12Gln missense_variant 0.46
embB 4246555 c.42G>C synonymous_variant 0.57
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4247512 c.999T>C synonymous_variant 0.12
embB 4247516 p.Asn335Asp missense_variant 0.12
embB 4248186 p.Leu558Ser missense_variant 0.1
embB 4249180 c.2667G>T synonymous_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.27
ethR 4326964 c.-585G>A upstream_gene_variant 0.24
ethR 4326970 c.-579G>T upstream_gene_variant 0.22
ethA 4327191 p.Asp95Tyr missense_variant 0.13
ethA 4327216 p.Lys86Asn missense_variant 0.17
ethA 4327530 c.-57G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408104 c.99G>T synonymous_variant 0.15