Run ID: SRR19428557
Sample name:
Date: 03-04-2023 21:40:06
Number of reads: 349568
Percentage reads mapped: 99.73
Strain: lineage3.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.06 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 0.27 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.81 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 0.73 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 0.77 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155388 | c.723delC | frameshift_variant | 0.13 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.31 |
gyrB | 6124 | c.885C>T | synonymous_variant | 0.27 |
gyrB | 6140 | p.Val301Leu | missense_variant | 0.67 |
gyrB | 6148 | c.911delT | frameshift_variant | 0.11 |
gyrA | 7168 | c.-134C>T | upstream_gene_variant | 0.17 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491226 | c.444C>T | synonymous_variant | 0.12 |
fgd1 | 491383 | c.602delA | frameshift_variant | 0.13 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.18 |
mshA | 575186 | c.-161delG | upstream_gene_variant | 0.12 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.17 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.17 |
rpoB | 762861 | p.Val1019Phe | missense_variant | 0.17 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.8 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775733 | c.2747delT | frameshift_variant | 0.18 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.26 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.11 |
mmpL5 | 776674 | p.Val603Met | missense_variant | 0.1 |
mmpL5 | 777905 | c.576G>T | synonymous_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781606 | p.Ile16Thr | missense_variant | 0.12 |
rplC | 801167 | c.360delC | frameshift_variant | 0.18 |
fbiC | 1302975 | c.45C>A | synonymous_variant | 0.17 |
fbiC | 1305413 | p.Lys828Arg | missense_variant | 0.15 |
Rv1258c | 1406349 | p.Ile331Ser | missense_variant | 0.25 |
Rv1258c | 1406724 | c.616delC | frameshift_variant | 0.1 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471984 | n.139T>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1475114 | n.1457C>T | non_coding_transcript_exon_variant | 0.55 |
fabG1 | 1673283 | c.-157A>C | upstream_gene_variant | 0.14 |
rpsA | 1833702 | p.Asp54Ala | missense_variant | 0.11 |
rpsA | 1834411 | c.870T>A | synonymous_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918435 | p.Ala166Thr | missense_variant | 0.22 |
katG | 2154456 | p.Ile552Met | missense_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.39 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.12 |
Rv1979c | 2222844 | c.321G>A | synonymous_variant | 0.1 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.67 |
eis | 2715028 | p.Ala102Val | missense_variant | 0.12 |
eis | 2715201 | c.131delG | frameshift_variant | 0.12 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.27 |
pepQ | 2860405 | c.13dupC | frameshift_variant | 0.18 |
ribD | 2987444 | c.606C>T | synonymous_variant | 0.13 |
ribD | 2987473 | p.Cys212Tyr | missense_variant | 0.11 |
Rv2752c | 3065323 | p.Ala290Val | missense_variant | 0.11 |
Rv2752c | 3065677 | p.Lys172Arg | missense_variant | 0.18 |
thyX | 3067853 | c.93C>A | synonymous_variant | 0.13 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.86 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087200 | c.381A>T | synonymous_variant | 0.12 |
fbiD | 3339099 | c.-19A>T | upstream_gene_variant | 0.13 |
Rv3083 | 3449073 | c.570C>T | synonymous_variant | 0.14 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475198 | p.Phe398Leu | missense_variant | 0.15 |
fprA | 3475327 | c.1324dupG | frameshift_variant | 0.2 |
whiB7 | 3568485 | c.195T>C | synonymous_variant | 0.13 |
whiB7 | 3568501 | c.178dupG | frameshift_variant | 0.12 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.87 |
Rv3236c | 3612148 | c.969G>A | synonymous_variant | 0.12 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.6 |
alr | 3841511 | c.-91C>A | upstream_gene_variant | 0.1 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.7 |
clpC1 | 4039004 | c.1701C>T | synonymous_variant | 0.13 |
clpC1 | 4040063 | c.642G>A | synonymous_variant | 0.18 |
clpC1 | 4040704 | c.1A>G | start_lost | 0.12 |
panD | 4043938 | p.Ile115Thr | missense_variant | 0.62 |
embC | 4241726 | p.Phe622Leu | missense_variant | 0.22 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.19 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242904 | p.Asp1014Glu | missense_variant | 0.2 |
embA | 4243235 | c.3G>A | synonymous_variant | 0.14 |
embA | 4243345 | p.Gln38Arg | missense_variant | 0.1 |
embA | 4243367 | c.137dupC | frameshift_variant | 0.12 |
embA | 4245046 | p.Leu605Pro | missense_variant | 0.12 |
embA | 4245166 | p.Pro645Gln | missense_variant | 0.21 |
embA | 4245768 | p.Asn846Asp | missense_variant | 0.29 |
embB | 4247575 | c.1062C>T | synonymous_variant | 0.1 |
embB | 4247578 | c.1065G>A | synonymous_variant | 0.1 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.1 |
embB | 4249264 | c.2754dupC | frameshift_variant | 0.18 |
aftB | 4268276 | c.561G>A | synonymous_variant | 0.15 |
aftB | 4268899 | c.-63G>T | upstream_gene_variant | 0.18 |
ubiA | 4269073 | p.Pro254Gln | missense_variant | 0.17 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338718 | c.-197C>T | upstream_gene_variant | 0.1 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.25 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.56 |