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
Drug | Resistance | Supporting mutations |
---|
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 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
tlyA | 1918211 | p.Ala91Glu | missense_variant | 0.12 | capreomycin |
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 |