Run ID: ERR909753
Sample name:
Date: 02-04-2023 09:28:01
Number of reads: 542162
Percentage reads mapped: 15.37
Strain: lineage5.1.1
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage5 | 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 |
---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.25 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5785 | c.546C>T | synonymous_variant | 0.12 |
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 | 7929 | p.Ala210Thr | missense_variant | 0.2 |
gyrA | 8954 | c.1653G>A | synonymous_variant | 0.14 |
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 |
gyrA | 9690 | p.Gln797Lys | missense_variant | 0.15 |
gyrA | 9780 | p.Ala827Ser | missense_variant | 0.12 |
fgd1 | 490751 | c.-32T>G | upstream_gene_variant | 0.18 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 619710 | c.-181G>T | upstream_gene_variant | 0.18 |
rpoB | 760567 | p.Ser254* | stop_gained | 0.18 |
rpoB | 761557 | p.Ala584Val | missense_variant | 0.33 |
rpoB | 761828 | c.2022C>T | synonymous_variant | 0.13 |
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 |
mmpL5 | 776474 | p.Met669Ile | missense_variant | 0.2 |
mmpL5 | 776487 | p.Gln665Arg | missense_variant | 0.18 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800938 | p.Arg44Ser | missense_variant | 0.15 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
fbiC | 1303463 | p.Ala178Glu | missense_variant | 0.25 |
Rv1258c | 1407121 | p.Val74Leu | missense_variant | 0.15 |
Rv1258c | 1407273 | p.Asp23Val | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473005 | n.1160C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474430 | n.773C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474488 | n.831G>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475107 | n.1450G>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1475892 | n.2235A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475897 | n.2240T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475900 | n.2243A>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475902 | n.2245T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475916 | n.2259C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476131 | n.2474C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476160 | n.2503T>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476559 | n.2902G>A | non_coding_transcript_exon_variant | 0.18 |
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 1.0 |
inhA | 1674194 | c.-8G>A | upstream_gene_variant | 0.22 |
inhA | 1674821 | p.Leu207Pro | missense_variant | 0.18 |
rpsA | 1834507 | c.966C>T | synonymous_variant | 0.15 |
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 | 2102449 | p.Lys198Asn | missense_variant | 0.22 |
ndh | 2102746 | c.297C>A | synonymous_variant | 0.29 |
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2156203 | c.-92C>T | upstream_gene_variant | 0.18 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169995 | c.618C>T | synonymous_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289018 | p.Gly75Val | missense_variant | 0.17 |
pncA | 2290039 | c.-798C>T | upstream_gene_variant | 0.15 |
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
pepQ | 2859498 | c.921C>T | synonymous_variant | 0.2 |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 1.0 |
Rv3083 | 3448825 | p.Glu108Lys | missense_variant | 0.12 |
Rv3083 | 3449118 | c.615G>A | synonymous_variant | 0.2 |
Rv3083 | 3449240 | p.Arg246His | missense_variant | 0.15 |
Rv3083 | 3449644 | p.Ala381Thr | missense_variant | 1.0 |
Rv3083 | 3449967 | c.1464G>A | synonymous_variant | 0.14 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474736 | p.Val244Ile | missense_variant | 0.17 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
Rv3236c | 3612162 | p.Ala319Thr | missense_variant | 0.25 |
Rv3236c | 3612919 | c.198C>A | synonymous_variant | 0.14 |
fbiB | 3640734 | c.-801C>G | upstream_gene_variant | 0.12 |
fbiB | 3642249 | p.Asp239Asn | missense_variant | 0.13 |
fbiB | 3642642 | p.His370Asn | missense_variant | 0.12 |
alr | 3840932 | c.489C>T | synonymous_variant | 1.0 |
rpoA | 3878169 | c.339G>A | synonymous_variant | 0.17 |
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 | 4039189 | p.Arg506Trp | missense_variant | 0.14 |
clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 1.0 |
panD | 4044446 | c.-165C>T | upstream_gene_variant | 1.0 |
embC | 4239843 | c.-20A>C | upstream_gene_variant | 1.0 |
embC | 4240354 | c.492C>A | synonymous_variant | 0.25 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4242772 | c.-461G>T | upstream_gene_variant | 0.4 |
embA | 4243899 | p.Ala223Thr | missense_variant | 0.13 |
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 |
embA | 4245227 | c.1995C>T | synonymous_variant | 0.18 |
embB | 4245587 | c.-927G>A | upstream_gene_variant | 0.15 |
embA | 4245645 | p.Ala805Thr | missense_variant | 0.17 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
aftB | 4267474 | p.Gly455Cys | missense_variant | 0.2 |
aftB | 4267876 | c.961C>T | synonymous_variant | 0.22 |
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 | 4338243 | c.279C>T | synonymous_variant | 0.17 |
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 |