Run ID: ERR2512474
Sample name:
Date: 31-03-2023 19:03:23
Number of reads: 953697
Percentage reads mapped: 99.31
Strain: lineage1.1.2
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 0.99 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155740 | c.371delG | frameshift_variant | 0.15 | isoniazid, isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6124 | c.885C>T | synonymous_variant | 1.0 |
gyrA | 7174 | c.-128C>T | upstream_gene_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 |
gyrA | 9658 | p.Thr786Ile | missense_variant | 0.12 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576387 | p.Ala347Val | missense_variant | 0.15 |
rpoB | 760490 | c.684C>T | synonymous_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 765450 | p.Ala694Val | missense_variant | 0.13 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776395 | p.Phe696Leu | missense_variant | 1.0 |
mmpL5 | 776694 | p.Val596Ser | missense_variant | 0.19 |
mmpL5 | 776702 | c.1779C>T | synonymous_variant | 0.21 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406519 | c.821delG | frameshift_variant | 0.12 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473717 | n.60G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476133 | n.2476G>A | non_coding_transcript_exon_variant | 0.15 |
fabG1 | 1673560 | p.Lys41Leu | missense_variant | 0.13 |
rpsA | 1834957 | c.1416C>A | synonymous_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154230 | p.Val628Ile | missense_variant | 0.33 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155170 | c.942C>A | synonymous_variant | 0.14 |
PPE35 | 2167745 | p.Thr956Arg | missense_variant | 0.21 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2169543 | p.Gly357Val | missense_variant | 0.12 |
PPE35 | 2169547 | p.His356Asn | missense_variant | 0.12 |
PPE35 | 2169548 | c.1065A>C | synonymous_variant | 0.12 |
PPE35 | 2169551 | c.1062C>G | synonymous_variant | 0.12 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.6 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.55 |
PPE35 | 2170247 | p.Ile122Met | missense_variant | 0.12 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518864 | c.750G>C | synonymous_variant | 0.18 |
kasA | 2518983 | p.Ala290Glu | missense_variant | 0.17 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.29 |
folC | 2746539 | p.His354Asn | missense_variant | 0.11 |
folC | 2747186 | c.403_412delGACCAGCAGT | frameshift_variant | 0.2 |
folC | 2747205 | c.393_394insCCC | conservative_inframe_insertion | 0.14 |
pepQ | 2860413 | c.6A>G | synonymous_variant | 0.15 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
thyX | 3067408 | p.Glu180Lys | missense_variant | 0.22 |
thyA | 3074144 | p.Asp110Tyr | missense_variant | 0.13 |
thyA | 3074361 | c.111T>C | synonymous_variant | 0.12 |
thyA | 3074514 | c.-43T>C | upstream_gene_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087071 | c.252C>A | synonymous_variant | 0.12 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449016 | c.513A>G | synonymous_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475128 | p.Asp374Glu | missense_variant | 0.17 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fbiB | 3642107 | c.573G>A | synonymous_variant | 0.17 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.25 |
ddn | 3986978 | c.135G>A | synonymous_variant | 0.12 |
clpC1 | 4040144 | c.561G>C | synonymous_variant | 0.18 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241458 | c.1596C>A | synonymous_variant | 0.12 |
embC | 4241931 | p.Thr690Ile | missense_variant | 0.14 |
embA | 4242613 | c.-620C>T | upstream_gene_variant | 0.12 |
embA | 4242616 | c.-617C>G | upstream_gene_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245218 | c.1986C>T | synonymous_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247002 | c.489G>T | synonymous_variant | 0.13 |
embB | 4247101 | c.588G>T | synonymous_variant | 0.15 |
embB | 4247470 | c.957T>C | synonymous_variant | 0.21 |
embB | 4247472 | p.Phe320Tyr | missense_variant | 0.23 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248335 | p.Ala608Thr | missense_variant | 0.13 |
ubiA | 4269031 | p.Gly268Asp | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
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 | 4407873 | c.330G>T | synonymous_variant | 1.0 |