Run ID: SRR11972414
Sample name:
Date: 03-04-2023 05:42:07
Number of reads: 596673
Percentage reads mapped: 99.21
Strain: lineage1.1.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
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 |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Tyr | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
thyA | 3074171 | p.Trp101Arg | missense_variant | 0.25 | para-aminosalicylic_acid |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6124 | c.885C>T | synonymous_variant | 1.0 |
gyrB | 6429 | p.Glu397Val | missense_variant | 0.14 |
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 | 9047 | c.1746C>T | synonymous_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9443 | c.2142G>A | synonymous_variant | 1.0 |
fgd1 | 491387 | p.Leu202Pro | missense_variant | 0.29 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575393 | p.Arg16Cys | missense_variant | 0.33 |
mshA | 576000 | p.Asp218Ala | missense_variant | 1.0 |
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 | 764027 | p.Glu220* | stop_gained | 0.17 |
rpoC | 764654 | p.Val429Leu | missense_variant | 0.12 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 767071 | c.3702C>T | synonymous_variant | 0.4 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776363 | c.2118A>G | synonymous_variant | 0.25 |
mmpL5 | 776395 | p.Phe696Leu | missense_variant | 1.0 |
mmpL5 | 777119 | p.His454Gln | missense_variant | 0.22 |
mmpL5 | 777122 | c.1359C>T | synonymous_variant | 0.22 |
mmpL5 | 777128 | c.1353A>G | synonymous_variant | 0.2 |
mmpR5 | 779390 | p.Arg134Leu | missense_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801313 | c.505C>A | synonymous_variant | 0.12 |
fbiC | 1303496 | p.Pro189Leu | missense_variant | 0.17 |
fbiC | 1304159 | p.Val410Gly | missense_variant | 0.4 |
fbiC | 1304826 | c.1900delT | frameshift_variant | 0.14 |
Rv1258c | 1406946 | p.Ala132Asp | missense_variant | 0.29 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474277 | n.620C>T | non_coding_transcript_exon_variant | 0.15 |
rpsA | 1834061 | p.Ile174Phe | missense_variant | 0.18 |
tlyA | 1917807 | c.-133T>G | upstream_gene_variant | 0.29 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154563 | p.Val517Phe | missense_variant | 0.22 |
katG | 2154631 | p.Gly494Asp | missense_variant | 0.25 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.33 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.31 |
PPE35 | 2170157 | p.Ala152Ser | missense_variant | 0.17 |
Rv1979c | 2222120 | p.Pro349Ser | 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 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
pepQ | 2859879 | p.Met180Ile | missense_variant | 0.17 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3064828 | p.Gly455Asp | missense_variant | 0.22 |
Rv2752c | 3065305 | p.Ala296Val | missense_variant | 1.0 |
Rv2752c | 3065949 | p.His81Gln | missense_variant | 0.13 |
thyA | 3073946 | p.Phe176Leu | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449355 | c.852C>T | synonymous_variant | 0.22 |
Rv3083 | 3449660 | p.Trp386* | stop_gained | 0.12 |
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 |
clpC1 | 4038475 | p.Ser744Cys | missense_variant | 0.12 |
clpC1 | 4038760 | p.Asp649Asn | missense_variant | 0.12 |
clpC1 | 4038780 | p.Leu642His | missense_variant | 0.14 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embA | 4246208 | c.2980delT | frameshift_variant | 0.17 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.4 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.3 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.3 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326069 | c.1405C>A | synonymous_variant | 0.25 |
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 |