Run ID: ERR2704707
Sample name:
Date: 31-03-2023 23:04:26
Number of reads: 297847
Percentage reads mapped: 99.15
Strain: lineage5.1.4
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage5 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 1.0 |
lineage5.1.4 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 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 | 7976 | c.675C>A | synonymous_variant | 0.2 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9566 | c.2265C>T | synonymous_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 620836 | p.Gly316Ser | missense_variant | 0.22 |
rpoB | 762619 | p.Trp938Leu | missense_variant | 0.25 |
rpoB | 762655 | p.Ala950Asp | missense_variant | 0.25 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763828 | c.459C>A | synonymous_variant | 0.17 |
rpoC | 764213 | c.844C>A | synonymous_variant | 0.2 |
rpoC | 765031 | p.Glu554Asp | missense_variant | 0.17 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775753 | c.2727delC | frameshift_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpR5 | 779275 | p.Arg96Trp | missense_variant | 0.29 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801354 | c.546G>T | synonymous_variant | 0.18 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
fbiC | 1304904 | p.Glu658Asp | missense_variant | 0.33 |
Rv1258c | 1406288 | c.1053G>T | synonymous_variant | 0.15 |
Rv1258c | 1406421 | p.Phe307Ser | missense_variant | 0.29 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.25 |
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101921 | c.1122G>A | synonymous_variant | 1.0 |
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169902 | c.711G>T | synonymous_variant | 0.25 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289626 | c.-385G>T | upstream_gene_variant | 0.25 |
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ribD | 2987181 | p.Pro115Thr | missense_variant | 0.22 |
thyX | 3067280 | c.666G>T | synonymous_variant | 0.2 |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 1.0 |
ald | 3087560 | c.741C>A | synonymous_variant | 0.17 |
Rv3083 | 3448734 | p.Asp77Glu | missense_variant | 0.25 |
Rv3083 | 3449080 | p.Val193Ile | missense_variant | 0.2 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
alr | 3840932 | c.489C>T | synonymous_variant | 1.0 |
alr | 3841138 | p.Asp95Tyr | missense_variant | 0.17 |
ddn | 3986987 | c.144G>T | synonymous_variant | 1.0 |
ddn | 3987180 | p.Asp113Asn | missense_variant | 1.0 |
clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 1.0 |
embC | 4239843 | c.-20A>C | upstream_gene_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241633 | p.Gly591Trp | missense_variant | 0.4 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242866 | p.Gly1002Cys | missense_variant | 0.2 |
embA | 4243181 | c.-52C>A | upstream_gene_variant | 0.29 |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
embA | 4244635 | p.Val468Ala | missense_variant | 1.0 |
embA | 4244858 | c.1626G>A | synonymous_variant | 0.17 |
embA | 4245147 | p.Pro639Ser | missense_variant | 1.0 |
embB | 4246526 | p.Ala5Ser | missense_variant | 0.25 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
aftB | 4267346 | c.1491C>T | synonymous_variant | 0.14 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269706 | p.Gly43Asp | missense_variant | 0.2 |
ethR | 4326928 | c.-621G>A | upstream_gene_variant | 1.0 |
ethA | 4327103 | p.Gly124Asp | missense_variant | 1.0 |
whiB6 | 4338546 | c.-25G>A | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |