Run ID: SRR998625
Sample name:
Date: 04-04-2023 23:28:43
Number of reads: 738490
Percentage reads mapped: 99.08
Strain: lineage6.3.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage6 | West-Africa 2 | AFRI_1 | RD702 | 0.4 |
lineage5.1.1 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 0.59 |
lineage6.3.1 | West-Africa 2 | AFRI_1 | RD702 | 0.36 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5070 | c.-170C>G | upstream_gene_variant | 0.13 |
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.95 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8885 | c.1584C>A | synonymous_variant | 0.17 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9566 | c.2265C>T | synonymous_variant | 0.62 |
fgd1 | 491668 | p.Lys296Glu | missense_variant | 0.5 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.94 |
ccsA | 620673 | p.Trp261Cys | missense_variant | 0.14 |
rpoB | 760969 | p.Ser388Leu | missense_variant | 0.5 |
rpoB | 761723 | p.Glu639Asp | missense_variant | 0.28 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763280 | c.-90C>T | upstream_gene_variant | 0.33 |
rpoC | 763904 | p.Ala179Ser | missense_variant | 0.47 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775841 | c.2640G>A | synonymous_variant | 0.14 |
mmpL5 | 776045 | c.2436G>A | synonymous_variant | 0.12 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.8 |
mmpL5 | 778684 | c.-204C>T | upstream_gene_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
Rv1258c | 1406740 | p.His201Tyr | missense_variant | 0.47 |
Rv1258c | 1407132 | p.Gly70Val | missense_variant | 0.12 |
Rv1258c | 1407205 | p.Ile46Val | missense_variant | 0.15 |
Rv1258c | 1407273 | p.Asp23Val | missense_variant | 0.5 |
embR | 1416401 | p.Asn316Ser | missense_variant | 0.14 |
embR | 1416989 | c.358delA | frameshift_variant | 0.18 |
atpE | 1461016 | c.-29C>A | upstream_gene_variant | 0.15 |
atpE | 1461050 | p.Asp2Glu | missense_variant | 0.12 |
atpE | 1461251 | c.207G>T | synonymous_variant | 0.26 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472135 | n.290C>T | non_coding_transcript_exon_variant | 0.12 |
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 0.6 |
inhA | 1674434 | p.Val78Ala | missense_variant | 0.29 |
rpsA | 1834171 | c.630C>G | synonymous_variant | 0.12 |
rpsA | 1834963 | c.1422G>T | synonymous_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101921 | c.1122G>A | synonymous_variant | 0.62 |
ndh | 2102694 | p.Val117Ile | missense_variant | 0.56 |
ndh | 2102967 | p.Gly26Trp | missense_variant | 0.12 |
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 0.58 |
katG | 2154465 | p.Cys549* | stop_gained | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.93 |
katG | 2155503 | c.609C>T | synonymous_variant | 0.5 |
katG | 2155995 | p.Trp39Cys | missense_variant | 0.25 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168625 | p.Thr663Asn | missense_variant | 0.11 |
PPE35 | 2169307 | p.Asp436Asn | missense_variant | 0.12 |
PPE35 | 2169715 | p.Gly300Ser | missense_variant | 0.18 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2222757 | c.408G>T | synonymous_variant | 0.33 |
Rv1979c | 2222852 | p.Ala105Thr | missense_variant | 0.67 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289888 | c.-647G>T | upstream_gene_variant | 0.25 |
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 0.69 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.85 |
kasA | 2518750 | p.Met212Ile | missense_variant | 0.13 |
pepQ | 2860083 | c.336C>T | synonymous_variant | 0.12 |
Rv2752c | 3065593 | p.Leu200Pro | missense_variant | 0.15 |
thyA | 3074664 | c.-193G>T | upstream_gene_variant | 0.11 |
ald | 3086728 | c.-92C>T | upstream_gene_variant | 0.47 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.43 |
ald | 3086856 | p.Glu13Lys | missense_variant | 0.38 |
ald | 3087084 | c.266delA | frameshift_variant | 0.94 |
ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 0.53 |
Rv3083 | 3448437 | c.-67C>G | upstream_gene_variant | 0.12 |
Rv3083 | 3449644 | p.Ala381Thr | missense_variant | 0.5 |
Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 0.5 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fprA | 3475343 | p.Ser446Ile | missense_variant | 0.11 |
fprA | 3475366 | p.Gly454Arg | missense_variant | 0.12 |
Rv3236c | 3612871 | p.Phe82Leu | missense_variant | 0.13 |
fbiB | 3641022 | c.-513C>A | upstream_gene_variant | 0.12 |
fbiB | 3641328 | c.-207T>C | upstream_gene_variant | 0.13 |
fbiB | 3641594 | c.60G>C | synonymous_variant | 0.12 |
alr | 3840932 | c.489C>T | synonymous_variant | 0.53 |
alr | 3841006 | p.Asp139Tyr | missense_variant | 0.12 |
rpoA | 3877696 | p.Thr271Ile | missense_variant | 0.25 |
rpoA | 3878493 | c.15G>A | synonymous_variant | 0.75 |
ddn | 3986987 | c.144G>T | synonymous_variant | 0.58 |
ddn | 3987180 | p.Asp113Asn | missense_variant | 0.83 |
clpC1 | 4040010 | p.Ala232Asp | missense_variant | 0.64 |
clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 0.85 |
panD | 4044306 | c.-25T>C | upstream_gene_variant | 0.22 |
embC | 4239843 | c.-20A>C | upstream_gene_variant | 0.17 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241843 | p.Leu661Ile | missense_variant | 0.5 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243493 | c.261C>G | synonymous_variant | 0.12 |
embA | 4244024 | p.Trp264Cys | missense_variant | 0.12 |
embA | 4244220 | c.988C>T | synonymous_variant | 0.9 |
embA | 4244379 | p.Pro383Ser | missense_variant | 0.38 |
embA | 4245147 | p.Pro639Ser | missense_variant | 0.45 |
embA | 4245657 | p.Ser809Pro | missense_variant | 0.18 |
embB | 4245908 | c.-606G>T | upstream_gene_variant | 0.15 |
embB | 4246864 | c.351C>T | synonymous_variant | 0.25 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
aftB | 4267411 | p.Gly476Arg | missense_variant | 0.11 |
aftB | 4268072 | p.Ile255Met | missense_variant | 0.11 |
aftB | 4268477 | c.360C>T | synonymous_variant | 0.65 |
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 0.38 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.93 |
aftB | 4269522 | c.-686C>T | upstream_gene_variant | 0.36 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.88 |
ubiA | 4270014 | c.-181C>G | upstream_gene_variant | 0.12 |
ethA | 4326465 | p.Ile337Val | missense_variant | 0.46 |
ethR | 4326928 | c.-621G>A | upstream_gene_variant | 0.5 |
ethA | 4327103 | p.Gly124Asp | missense_variant | 0.36 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407734 | p.Gly157Arg | missense_variant | 0.15 |
gid | 4407847 | p.Ala119Asp | missense_variant | 0.13 |
gid | 4408327 | c.-125A>G | upstream_gene_variant | 0.23 |