Run ID: SRR11972166
Sample name:
Date: 03-04-2023 05:30:37
Number of reads: 598319
Percentage reads mapped: 98.46
Strain: lineage1.1.3.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 1.0 |
lineage1.1.3.1 | Indo-Oceanic | NA | RD239 | 0.58 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576459 | c.1117_1147delGCGGTGGGCGGGCTGCCCGTCGCGGTGCGCG | frameshift_variant | 0.67 |
mshA | 576544 | c.1197C>A | synonymous_variant | 0.5 |
ccsA | 620839 | p.Leu317Met | missense_variant | 0.12 |
rpoB | 760862 | c.1056G>T | synonymous_variant | 0.17 |
rpoB | 761152 | p.Leu449Gln | missense_variant | 0.2 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763223 | c.-147C>A | upstream_gene_variant | 0.18 |
rpoC | 763834 | p.Met155Ile | missense_variant | 0.33 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764040 | p.Ser224Ile | missense_variant | 0.2 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 1.0 |
rpoC | 766228 | p.Leu953Phe | missense_variant | 0.18 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776006 | c.2475C>T | synonymous_variant | 0.31 |
mmpL5 | 776009 | c.2472A>G | synonymous_variant | 0.15 |
mmpL5 | 776018 | c.2463G>C | synonymous_variant | 0.29 |
mmpL5 | 776021 | c.2460G>C | synonymous_variant | 0.27 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776194 | p.Ala763Thr | missense_variant | 0.2 |
mmpL5 | 776407 | p.Pro692Ser | missense_variant | 0.15 |
mmpL5 | 776429 | c.2052C>A | synonymous_variant | 0.14 |
mmpL5 | 776826 | p.Glu552Gly | missense_variant | 0.35 |
mmpL5 | 777172 | p.His437Asn | missense_variant | 0.13 |
mmpL5 | 777739 | p.Ala248Thr | missense_variant | 0.15 |
mmpL5 | 777911 | c.570C>T | synonymous_variant | 0.22 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472184 | n.339T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472193 | n.348A>G | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.65 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472333 | n.488G>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472350 | n.505C>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472373 | n.528G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472815 | n.970A>C | non_coding_transcript_exon_variant | 0.56 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.4 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154136 | p.Val659Glu | missense_variant | 0.13 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167814 | c.2799C>T | synonymous_variant | 0.27 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2168124 | p.Gly830Glu | missense_variant | 0.2 |
PPE35 | 2168357 | c.2256T>C | synonymous_variant | 0.14 |
PPE35 | 2168895 | p.Gly573Val | missense_variant | 0.14 |
PPE35 | 2169269 | c.1344A>G | synonymous_variant | 0.4 |
PPE35 | 2169272 | c.1341C>G | synonymous_variant | 0.36 |
PPE35 | 2169278 | c.1335T>C | synonymous_variant | 0.3 |
PPE35 | 2169281 | c.1332T>G | synonymous_variant | 0.3 |
PPE35 | 2169287 | c.1326T>C | synonymous_variant | 0.19 |
PPE35 | 2169630 | p.Asn328Ser | missense_variant | 0.46 |
PPE35 | 2169757 | p.Asn286Asp | missense_variant | 0.31 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.5 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.47 |
PPE35 | 2170147 | p.Ser156Ala | missense_variant | 0.21 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289921 | c.-680A>T | upstream_gene_variant | 0.13 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518495 | p.Asp127Glu | missense_variant | 0.22 |
kasA | 2519338 | c.1224T>C | synonymous_variant | 0.5 |
eis | 2715305 | p.Glu10* | stop_gained | 0.56 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726341 | p.Val50Gly | missense_variant | 0.27 |
folC | 2746872 | p.Glu243* | stop_gained | 0.22 |
folC | 2747420 | p.Pro60His | missense_variant | 0.18 |
pepQ | 2859373 | p.Pro349Gln | missense_variant | 0.18 |
ribD | 2986995 | p.Ala53Thr | missense_variant | 0.18 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3064803 | c.1389C>A | synonymous_variant | 0.4 |
Rv2752c | 3067111 | c.-920G>T | upstream_gene_variant | 0.13 |
thyA | 3074648 | c.-177T>G | upstream_gene_variant | 0.3 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449041 | p.Val180Ile | missense_variant | 0.25 |
Rv3083 | 3449046 | c.543C>G | synonymous_variant | 0.29 |
Rv3083 | 3449364 | c.861C>A | synonymous_variant | 0.14 |
Rv3083 | 3449393 | p.Leu297Ser | missense_variant | 0.17 |
Rv3083 | 3449709 | c.1206C>G | synonymous_variant | 0.59 |
Rv3083 | 3449968 | p.Ala489Thr | missense_variant | 0.25 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568419 | c.261C>T | synonymous_variant | 0.57 |
Rv3236c | 3612999 | p.Gly40Cys | missense_variant | 0.13 |
fbiB | 3642371 | c.837G>T | synonymous_variant | 0.5 |
alr | 3840425 | c.995dupG | frameshift_variant | 0.13 |
alr | 3840493 | c.928C>T | synonymous_variant | 0.58 |
alr | 3841253 | c.168C>T | synonymous_variant | 0.5 |
alr | 3841349 | c.72C>A | synonymous_variant | 0.3 |
clpC1 | 4039161 | p.His515Gly | missense_variant | 0.13 |
clpC1 | 4039169 | p.Glu512Asp | missense_variant | 0.36 |
clpC1 | 4039691 | c.1014G>C | synonymous_variant | 0.18 |
clpC1 | 4039948 | p.Gly253* | stop_gained | 0.13 |
clpC1 | 4040057 | c.648C>T | synonymous_variant | 0.27 |
clpC1 | 4040246 | c.459C>T | synonymous_variant | 0.33 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
panD | 4043901 | c.381C>T | synonymous_variant | 0.12 |
embC | 4240207 | c.345G>A | synonymous_variant | 0.45 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241792 | p.Ser644Pro | missense_variant | 0.2 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4243876 | p.Leu215Pro | missense_variant | 0.14 |
embA | 4244845 | p.Arg538Pro | missense_variant | 0.33 |
embA | 4245603 | p.Gly791Trp | missense_variant | 0.5 |
embA | 4245853 | p.Ala874Val | missense_variant | 0.33 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4246567 | c.54_55insT | frameshift_variant | 0.4 |
embB | 4247039 | p.Phe176Val | missense_variant | 0.17 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248552 | p.Ala680Asp | missense_variant | 0.12 |
embB | 4249053 | p.Thr847Asn | missense_variant | 0.2 |
aftB | 4267431 | p.Ser469Leu | missense_variant | 0.47 |
aftB | 4268639 | c.198G>A | synonymous_variant | 0.4 |
aftB | 4268900 | c.-64C>A | upstream_gene_variant | 0.25 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethR | 4326961 | c.-588G>C | upstream_gene_variant | 0.15 |
ethR | 4326964 | c.-585G>A | upstream_gene_variant | 0.2 |
ethR | 4326970 | c.-579G>T | upstream_gene_variant | 0.22 |
whiB6 | 4338210 | p.Tyr104* | stop_gained | 0.33 |
whiB6 | 4338213 | c.309T>G | synonymous_variant | 0.33 |
whiB6 | 4338217 | p.Asn102Thr | missense_variant | 0.33 |
whiB6 | 4338343 | p.Trp60* | stop_gained | 0.4 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407780 | c.423G>A | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4408464 | c.-262G>A | upstream_gene_variant | 0.6 |