Run ID: SRR11972165
Sample name:
Date: 03-04-2023 05:30:18
Number of reads: 518981
Percentage reads mapped: 99.07
Strain: lineage2.2.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.99 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.97 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761161 | p.Leu452Pro | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6590 | p.Arg451Ser | missense_variant | 0.14 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9531 | p.Gly744Ser | missense_variant | 0.22 |
gyrA | 9791 | c.2490C>T | synonymous_variant | 0.33 |
fgd1 | 491152 | p.Glu124Gln | missense_variant | 0.15 |
fgd1 | 491158 | p.Lys126Glu | missense_variant | 0.15 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 619831 | c.-60T>G | upstream_gene_variant | 0.5 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 760601 | p.Asp265Glu | missense_variant | 0.4 |
rpoB | 761082 | p.Gly426Cys | missense_variant | 0.29 |
rpoB | 762726 | p.Ala974Thr | missense_variant | 0.5 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776018 | c.2463G>C | synonymous_variant | 0.33 |
mmpL5 | 776021 | c.2460G>C | synonymous_variant | 0.33 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 776430 | p.Arg684Pro | missense_variant | 0.13 |
mmpL5 | 777191 | c.1290C>A | synonymous_variant | 0.2 |
mmpL5 | 777196 | p.Glu429Gln | missense_variant | 0.22 |
mmpL5 | 778101 | p.Gln127Arg | missense_variant | 0.29 |
mmpL5 | 778489 | c.-9G>A | upstream_gene_variant | 0.25 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302821 | c.-110G>A | upstream_gene_variant | 0.17 |
fbiC | 1303151 | p.Gly74Asp | missense_variant | 0.29 |
fbiC | 1303273 | p.Arg115Ser | missense_variant | 0.18 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
embR | 1416480 | p.Ala290Ser | missense_variant | 0.17 |
embR | 1417526 | c.-179G>T | upstream_gene_variant | 0.5 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472333 | n.488G>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472350 | n.505C>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472373 | n.528G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472591 | n.746G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474084 | n.431delA | non_coding_transcript_exon_variant | 0.22 |
fabG1 | 1673346 | c.-94C>G | upstream_gene_variant | 0.15 |
fabG1 | 1673349 | c.-91G>C | upstream_gene_variant | 0.15 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.21 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.21 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.21 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.37 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834264 | c.723G>T | synonymous_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102668 | c.375T>C | synonymous_variant | 0.17 |
ndh | 2102671 | c.372T>C | synonymous_variant | 0.17 |
ndh | 2102875 | c.168C>T | synonymous_variant | 0.12 |
ndh | 2102912 | p.Ala44Val | missense_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2154977 | p.Ala379Thr | missense_variant | 0.17 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.33 |
PPE35 | 2167967 | c.2646A>C | synonymous_variant | 0.36 |
PPE35 | 2169890 | c.723C>T | synonymous_variant | 0.15 |
PPE35 | 2169893 | c.720C>A | synonymous_variant | 0.17 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.22 |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.15 |
PPE35 | 2169974 | c.639T>C | synonymous_variant | 0.17 |
PPE35 | 2170147 | p.Ser156Ala | missense_variant | 0.15 |
PPE35 | 2170159 | p.Ala152Ser | missense_variant | 0.2 |
PPE35 | 2170392 | p.Gly74Ala | missense_variant | 0.22 |
PPE35 | 2170400 | c.213G>C | synonymous_variant | 0.18 |
PPE35 | 2170403 | c.210C>A | synonymous_variant | 0.18 |
PPE35 | 2170406 | c.207A>G | synonymous_variant | 0.26 |
Rv1979c | 2222145 | p.Leu340Phe | missense_variant | 0.17 |
Rv1979c | 2222200 | p.Gly322Asp | missense_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289733 | c.-492G>A | upstream_gene_variant | 0.33 |
pncA | 2289855 | c.-614G>A | upstream_gene_variant | 1.0 |
kasA | 2518151 | p.Ser13Arg | missense_variant | 0.33 |
kasA | 2518456 | c.342C>T | synonymous_variant | 0.25 |
kasA | 2518879 | c.765A>G | synonymous_variant | 0.2 |
kasA | 2518882 | c.768C>A | synonymous_variant | 0.2 |
kasA | 2519128 | c.1014G>C | synonymous_variant | 0.29 |
kasA | 2519131 | c.1017G>C | synonymous_variant | 0.29 |
eis | 2714846 | p.Val163Ile | missense_variant | 1.0 |
eis | 2715364 | c.-32C>A | upstream_gene_variant | 0.4 |
ahpC | 2726341 | p.Val50Gly | missense_variant | 0.25 |
ribD | 2986657 | c.-182C>T | upstream_gene_variant | 0.25 |
thyA | 3073696 | p.Ala259Asp | missense_variant | 0.14 |
thyA | 3073777 | p.Leu232Pro | missense_variant | 0.14 |
thyA | 3074580 | c.-109T>C | upstream_gene_variant | 0.33 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475102 | p.Gly366Arg | missense_variant | 0.25 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiA | 3640757 | p.Gly72Val | missense_variant | 0.15 |
fbiB | 3642787 | p.Trp418Leu | missense_variant | 0.33 |
alr | 3840414 | p.Pro336His | missense_variant | 0.4 |
alr | 3840603 | p.Pro273Leu | missense_variant | 0.18 |
rpoA | 3877812 | c.696C>A | synonymous_variant | 1.0 |
clpC1 | 4039161 | p.His515Gly | missense_variant | 0.12 |
clpC1 | 4039372 | p.Glu445* | stop_gained | 0.4 |
clpC1 | 4039594 | p.Arg371Gly | missense_variant | 0.22 |
clpC1 | 4039645 | p.His354Asp | missense_variant | 0.17 |
clpC1 | 4039754 | c.951G>A | synonymous_variant | 0.17 |
clpC1 | 4039829 | p.Leu292Ile | missense_variant | 0.2 |
clpC1 | 4040144 | c.561G>C | synonymous_variant | 0.29 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.33 |
embB | 4246567 | c.54_55insT | frameshift_variant | 0.4 |
embB | 4248115 | c.1602C>T | synonymous_variant | 0.82 |
embB | 4249348 | c.2835G>A | synonymous_variant | 0.4 |
aftB | 4267606 | p.Arg411Ser | missense_variant | 0.2 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267881 | p.Gly319Val | missense_variant | 0.4 |
aftB | 4268279 | c.556_557delCG | frameshift_variant | 0.15 |
ubiA | 4269295 | p.Met180Thr | missense_variant | 0.5 |
ethA | 4326557 | p.Arg306Leu | missense_variant | 0.17 |
ethR | 4326961 | c.-588G>C | upstream_gene_variant | 0.12 |
ethR | 4326970 | c.-579G>T | upstream_gene_variant | 0.12 |
ethA | 4327092 | p.Ala128Thr | missense_variant | 0.17 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407643 | p.Arg187Lys | missense_variant | 0.22 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |