Run ID: ERR1082126
Sample name:
Date: 15-08-2022 11:26:45
Number of reads: 5179082
Percentage reads mapped: 74.43
Strain: lineage5.1.1
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 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 1.0 |
lineage5.1.1 | 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 | 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 | 0.99 |
rpoB | 761931 | c.2125C>T | synonymous_variant | 0.99 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763280 | c.-90C>T | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
Rv1258c | 1407273 | p.Asp23Val | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472541 | n.696T>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472544 | n.699C>G | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472573 | n.728C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.9 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.9 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.9 |
rrl | 1474830 | n.1173A>T | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474831 | n.1174A>T | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474839 | n.1182C>T | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.8 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.3 |
rrl | 1475866 | n.2209T>A | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475869 | n.2212C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475877 | n.2220C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475880 | n.2223C>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475881 | n.2224T>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475882 | n.2225C>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475897 | n.2240T>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.64 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476573 | n.2916A>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.2 |
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 1.0 |
inhA | 1673568 | c.-634C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101840 | c.1203G>A | 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 | 2169315 | p.Asn433Ser | missense_variant | 0.99 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 1.0 |
Rv3083 | 3449644 | p.Ala381Thr | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.99 |
alr | 3840932 | c.489C>T | synonymous_variant | 1.0 |
rpoA | 3878493 | c.15G>A | synonymous_variant | 1.0 |
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 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
embA | 4244635 | p.Val468Ala | missense_variant | 1.0 |
embA | 4245147 | p.Pro639Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethR | 4326928 | c.-621G>A | upstream_gene_variant | 1.0 |
ethA | 4327103 | p.Gly124Asp | missense_variant | 1.0 |
whiB6 | 4338547 | c.-26A>G | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |