Run ID: ERR9891997
Sample name:
Date: 02-04-2023 13:26:53
Number of reads: 550677
Percentage reads mapped: 98.7
Strain: lineage6.3.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage6 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
lineage6.3 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
lineage6.3.1 | West-Africa 2 | AFRI_1 | RD702 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9113 | c.1812C>A | synonymous_variant | 0.12 |
gyrA | 9116 | p.Glu605Asp | missense_variant | 0.12 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9232 | p.Arg644Leu | missense_variant | 0.4 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9581 | c.2280C>T | synonymous_variant | 0.29 |
gyrA | 9591 | p.Gly764Arg | missense_variant | 1.0 |
fgd1 | 491128 | p.Thr116Ser | missense_variant | 0.2 |
fgd1 | 491433 | c.651C>T | synonymous_variant | 0.22 |
fgd1 | 491668 | p.Lys296Glu | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575249 | c.-99G>T | upstream_gene_variant | 0.2 |
mshA | 576408 | p.Ser354Leu | missense_variant | 0.5 |
mshA | 576462 | p.Ala372Glu | missense_variant | 0.25 |
mshA | 576615 | p.Arg423Leu | missense_variant | 0.25 |
ccsA | 620006 | p.Val39Gly | missense_variant | 0.5 |
ccsA | 620550 | c.660C>A | synonymous_variant | 0.22 |
rpoB | 759991 | p.Pro62Arg | missense_variant | 0.1 |
rpoB | 760969 | p.Ser388Leu | missense_variant | 1.0 |
rpoB | 761654 | p.Glu616Asp | missense_variant | 0.18 |
rpoB | 761723 | p.Glu639Asp | missense_variant | 1.0 |
rpoC | 762626 | c.-744C>G | upstream_gene_variant | 0.29 |
rpoB | 762751 | p.Leu982Gln | missense_variant | 0.18 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763614 | p.Val82Glu | missense_variant | 0.14 |
rpoC | 764332 | c.963G>A | synonymous_variant | 0.25 |
rpoC | 764890 | c.1521G>A | synonymous_variant | 0.12 |
rpoC | 765181 | c.1812G>T | synonymous_variant | 0.25 |
rpoC | 765388 | c.2020_2030delAACGAGCTGCT | frameshift_variant | 0.2 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776091 | p.Ser797Ile | missense_variant | 0.13 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776405 | c.2073_2075delGCC | disruptive_inframe_deletion | 0.18 |
mmpL5 | 776452 | p.Gly677Arg | missense_variant | 0.17 |
mmpL5 | 776546 | p.Met645Ile | missense_variant | 0.17 |
mmpL5 | 776617 | p.Pro622Thr | missense_variant | 0.11 |
mmpL5 | 776715 | p.Lys589Arg | missense_variant | 0.14 |
mmpL5 | 776953 | p.Leu510Met | missense_variant | 0.2 |
mmpL5 | 777145 | p.Glu446Lys | missense_variant | 0.2 |
mmpL5 | 777201 | p.Ala427Asp | missense_variant | 0.17 |
mmpR5 | 779288 | p.Phe100Ser | missense_variant | 0.11 |
mmpR5 | 779398 | c.412delG | frameshift_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801215 | p.Gly136Asp | missense_variant | 0.18 |
fbiC | 1302893 | c.-38G>C | upstream_gene_variant | 0.13 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
fbiC | 1303337 | p.Ala136Asp | missense_variant | 0.12 |
fbiC | 1303419 | c.489C>A | synonymous_variant | 0.12 |
fbiC | 1304196 | c.1266C>A | synonymous_variant | 0.14 |
fbiC | 1304907 | c.1977C>A | synonymous_variant | 0.12 |
fbiC | 1305484 | p.Ala852Ser | missense_variant | 0.33 |
Rv1258c | 1406325 | p.Arg339Gln | missense_variant | 0.2 |
Rv1258c | 1406884 | p.Ala153Ser | missense_variant | 0.13 |
embR | 1416786 | p.Ser188Gly | missense_variant | 0.22 |
atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1673716 | p.Ala93Pro | missense_variant | 0.25 |
fabG1 | 1674107 | p.Phe223Tyr | missense_variant | 0.15 |
inhA | 1674434 | p.Val78Ala | missense_variant | 1.0 |
inhA | 1674713 | p.Val171Gly | missense_variant | 0.12 |
rpsA | 1834526 | p.Arg329Ser | missense_variant | 0.13 |
rpsA | 1834884 | p.Gln448Arg | missense_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101777 | c.1266C>A | synonymous_variant | 0.33 |
ndh | 2102299 | p.Met248Ile | missense_variant | 0.33 |
ndh | 2102694 | p.Val117Ile | missense_variant | 1.0 |
katG | 2154619 | p.Arg498Leu | missense_variant | 0.14 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155069 | p.Ala348Asp | missense_variant | 0.12 |
katG | 2155451 | p.Ala221Ser | missense_variant | 0.29 |
katG | 2155503 | c.609C>T | synonymous_variant | 1.0 |
katG | 2156043 | c.69G>T | synonymous_variant | 0.22 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170435 | c.178C>A | synonymous_variant | 0.12 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2222852 | p.Ala105Thr | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288878 | p.Gln122Lys | missense_variant | 0.14 |
pncA | 2289008 | c.234C>A | synonymous_variant | 0.12 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518370 | p.Met86Leu | missense_variant | 0.17 |
kasA | 2518439 | p.Ala109Ser | missense_variant | 0.17 |
folC | 2746838 | p.Ala254Glu | missense_variant | 0.13 |
pepQ | 2860426 | c.-8C>T | upstream_gene_variant | 0.12 |
ribD | 2986963 | p.Arg42Pro | missense_variant | 0.14 |
Rv2752c | 3065284 | p.Ile303Asn | missense_variant | 0.14 |
Rv2752c | 3066096 | c.96G>A | synonymous_variant | 0.14 |
thyX | 3067331 | p.Asp205Glu | missense_variant | 0.25 |
thyX | 3067757 | c.189C>T | synonymous_variant | 0.2 |
thyX | 3067888 | p.Pro20Thr | missense_variant | 0.2 |
thyX | 3067965 | c.-20C>A | upstream_gene_variant | 0.17 |
thyA | 3074135 | p.Ser113Cys | missense_variant | 0.12 |
ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
ald | 3087669 | p.Asp284Tyr | missense_variant | 0.12 |
ald | 3087788 | p.Glu323Asp | missense_variant | 0.11 |
ald | 3087890 | c.1071C>A | synonymous_variant | 0.12 |
fbiD | 3339709 | p.Ala198Ser | missense_variant | 0.4 |
Rv3083 | 3448725 | c.222G>T | synonymous_variant | 0.2 |
Rv3083 | 3449122 | p.Val207Met | missense_variant | 0.33 |
Rv3083 | 3449371 | p.Tyr290His | missense_variant | 0.22 |
Rv3083 | 3449454 | c.951G>A | synonymous_variant | 0.2 |
Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475108 | p.Ile368Phe | missense_variant | 0.5 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568597 | p.Trp28Leu | missense_variant | 0.18 |
whiB7 | 3568641 | c.39A>G | synonymous_variant | 0.2 |
whiB7 | 3568686 | c.-7A>G | upstream_gene_variant | 0.25 |
Rv3236c | 3612015 | c.1101delG | frameshift_variant | 0.25 |
Rv3236c | 3612606 | p.Val171Phe | missense_variant | 0.14 |
Rv3236c | 3612685 | c.432C>A | synonymous_variant | 0.17 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.12 |
Rv3236c | 3613153 | c.-37G>T | upstream_gene_variant | 0.11 |
fbiB | 3640875 | c.-660C>G | upstream_gene_variant | 0.12 |
fbiB | 3641178 | c.-357G>T | upstream_gene_variant | 0.18 |
fbiB | 3641858 | c.324G>A | synonymous_variant | 0.22 |
fbiB | 3642125 | p.Glu197Asp | missense_variant | 0.33 |
fbiB | 3642138 | p.Ala202Ser | missense_variant | 0.25 |
fbiB | 3642630 | p.Thr366Ser | missense_variant | 0.12 |
fbiB | 3642637 | p.Ala368Gly | missense_variant | 0.11 |
fbiB | 3642639 | c.1107_1111delGCACA | frameshift_variant | 0.11 |
fbiB | 3642648 | p.Met372Val | missense_variant | 0.11 |
fbiB | 3642651 | p.Phe373Asn | missense_variant | 0.12 |
fbiB | 3642655 | p.Thr374Met | missense_variant | 0.12 |
fbiB | 3642657 | c.1124_1125insGTGCT | frameshift_variant | 0.12 |
fbiB | 3642661 | p.Ala376Gly | missense_variant | 0.12 |
fbiB | 3642668 | c.1134A>T | synonymous_variant | 0.12 |
alr | 3841369 | p.Arg18Trp | missense_variant | 0.12 |
rpoA | 3877696 | p.Thr271Ile | missense_variant | 1.0 |
rpoA | 3877758 | c.750G>T | synonymous_variant | 0.25 |
rpoA | 3878223 | p.Met95Ile | missense_variant | 0.17 |
rpoA | 3878475 | p.Glu11Asp | missense_variant | 0.15 |
ddn | 3986681 | c.-163C>A | upstream_gene_variant | 0.25 |
clpC1 | 4038684 | p.Ser674Tyr | missense_variant | 0.14 |
clpC1 | 4040834 | c.-130G>T | upstream_gene_variant | 0.12 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4240689 | p.Leu276Gln | missense_variant | 0.25 |
embC | 4241843 | p.Leu661Ile | missense_variant | 1.0 |
embC | 4241905 | p.Phe681Leu | missense_variant | 0.22 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 |
embA | 4245561 | p.Val777Leu | missense_variant | 0.33 |
embB | 4246528 | c.15G>A | synonymous_variant | 1.0 |
embB | 4246817 | p.Ala102Thr | missense_variant | 0.22 |
embB | 4246842 | p.Asn110Ile | missense_variant | 0.12 |
embB | 4246864 | c.351C>T | synonymous_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248902 | p.Thr797Ala | missense_variant | 0.18 |
aftB | 4268477 | c.360C>T | synonymous_variant | 1.0 |
ubiA | 4269068 | p.Thr256Ala | missense_variant | 0.33 |
ubiA | 4269127 | p.Trp236Leu | missense_variant | 0.14 |
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 0.94 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269522 | c.-686C>T | upstream_gene_variant | 0.75 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.75 |
ubiA | 4269667 | p.Ser56Trp | missense_variant | 0.18 |
ubiA | 4269855 | c.-22G>T | upstream_gene_variant | 0.13 |
ethA | 4326241 | p.Asp411Glu | missense_variant | 1.0 |
ethA | 4326465 | p.Ile337Val | missense_variant | 1.0 |
whiB6 | 4338478 | p.Phe15Ser | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338658 | c.-137G>A | upstream_gene_variant | 0.17 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407973 | p.Val77Ala | missense_variant | 0.14 |
gid | 4408215 | c.-13G>T | upstream_gene_variant | 0.13 |