Run ID: ERR2229371
Sample name:
Date: 31-03-2023 17:07:26
Number of reads: 978124
Percentage reads mapped: 98.8
Strain: lineage4.8
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 7160 | p.Ala641Thr | missense_variant | 0.25 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8668 | p.Ala456Asp | missense_variant | 0.17 |
gyrA | 9221 | c.1920C>T | synonymous_variant | 0.22 |
fgd1 | 490957 | p.Thr59Ser | missense_variant | 0.14 |
fgd1 | 491066 | c.286delC | frameshift_variant | 0.12 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.33 |
mshA | 576111 | p.Ala255Gly | missense_variant | 0.22 |
mshA | 576114 | p.Arg256Pro | missense_variant | 0.33 |
ccsA | 619958 | p.Val23Ala | missense_variant | 0.22 |
ccsA | 620274 | c.384G>T | synonymous_variant | 0.22 |
ccsA | 620341 | p.Val151Leu | missense_variant | 0.15 |
rpoB | 759715 | c.-92G>T | upstream_gene_variant | 0.33 |
rpoB | 760937 | c.1131G>A | synonymous_variant | 0.14 |
rpoB | 761152 | p.Leu449Gln | missense_variant | 0.25 |
rpoB | 761749 | p.Ser648* | stop_gained | 0.14 |
rpoB | 761814 | p.Ala670Pro | missense_variant | 0.2 |
rpoB | 762280 | p.Glu825Gly | missense_variant | 0.14 |
rpoC | 764877 | p.Thr503Asn | missense_variant | 0.13 |
rpoC | 765058 | p.Asn563Lys | missense_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775741 | c.2740C>T | synonymous_variant | 0.14 |
mmpL5 | 775747 | p.Met912Leu | missense_variant | 0.12 |
mmpL5 | 777157 | c.1324C>A | synonymous_variant | 0.18 |
mmpL5 | 777164 | c.1317C>T | synonymous_variant | 0.22 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781483 | c.-77C>T | upstream_gene_variant | 0.12 |
fbiC | 1303109 | p.Ala60Glu | missense_variant | 0.18 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
fbiC | 1305105 | c.2175G>T | synonymous_variant | 0.18 |
embR | 1417422 | c.-75C>A | upstream_gene_variant | 0.13 |
embR | 1417479 | c.-132G>A | upstream_gene_variant | 0.13 |
embR | 1417484 | c.-137C>A | upstream_gene_variant | 0.13 |
atpE | 1460868 | c.-177A>G | upstream_gene_variant | 0.13 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472485 | n.640G>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1473714 | n.57C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1673167 | c.-273G>T | upstream_gene_variant | 0.12 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.12 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.12 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.12 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.27 |
fabG1 | 1673986 | p.Pro183Ser | missense_variant | 0.13 |
inhA | 1674811 | p.Gly204Ser | missense_variant | 0.15 |
tlyA | 1917898 | c.-42T>C | upstream_gene_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918249 | p.Gly104Ser | missense_variant | 0.14 |
ndh | 2102558 | p.Ser162Ile | missense_variant | 0.33 |
ndh | 2102625 | p.Ser140Thr | missense_variant | 0.14 |
ndh | 2102632 | c.411C>A | synonymous_variant | 0.14 |
ndh | 2102638 | c.405A>G | synonymous_variant | 0.14 |
ndh | 2102649 | p.Ala132Ser | missense_variant | 0.14 |
ndh | 2102701 | p.Ser114Arg | missense_variant | 0.14 |
katG | 2154928 | p.Arg395Pro | missense_variant | 0.17 |
katG | 2154993 | c.1119C>A | synonymous_variant | 0.15 |
PPE35 | 2167745 | p.Thr956Arg | missense_variant | 0.14 |
PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.13 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.65 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.72 |
Rv1979c | 2221735 | p.Arg477Gln | missense_variant | 0.13 |
Rv1979c | 2222093 | p.Ser358Pro | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518606 | c.492G>C | synonymous_variant | 0.33 |
kasA | 2518609 | p.Met165Ile | missense_variant | 0.29 |
kasA | 2518809 | p.Lys232Arg | missense_variant | 0.24 |
kasA | 2518864 | c.750G>C | synonymous_variant | 0.14 |
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.4 |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.4 |
ahpC | 2726556 | p.Ala122Thr | missense_variant | 0.12 |
pepQ | 2859766 | p.Val218Ala | missense_variant | 0.18 |
thyX | 3067340 | c.606G>A | synonymous_variant | 0.14 |
ald | 3087166 | p.Ala116Gly | missense_variant | 0.22 |
fprA | 3474435 | c.429C>T | synonymous_variant | 0.14 |
fprA | 3474869 | p.Val288Ala | missense_variant | 0.15 |
fprA | 3475221 | p.Gln405His | missense_variant | 0.14 |
Rv3236c | 3612577 | p.Glu180Asp | missense_variant | 0.14 |
Rv3236c | 3612873 | p.Phe82Leu | missense_variant | 0.17 |
Rv3236c | 3613192 | c.-76G>A | upstream_gene_variant | 0.14 |
fbiB | 3641708 | c.174C>T | synonymous_variant | 0.13 |
alr | 3840392 | p.Met343Ile | missense_variant | 0.12 |
alr | 3840463 | c.958C>A | synonymous_variant | 0.14 |
rpoA | 3878492 | p.Arg6Ser | missense_variant | 0.14 |
clpC1 | 4039594 | p.Arg371Gly | missense_variant | 0.18 |
clpC1 | 4039602 | p.Ala368Val | missense_variant | 0.18 |
clpC1 | 4039645 | p.His354Asp | missense_variant | 0.13 |
clpC1 | 4039654 | p.Thr351Ser | missense_variant | 0.14 |
embC | 4240357 | c.495C>A | synonymous_variant | 0.15 |
embC | 4240617 | p.Asp252Val | missense_variant | 0.14 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242825 | p.Gly988Ala | missense_variant | 0.12 |
embA | 4244667 | p.Val479Leu | missense_variant | 0.17 |
embA | 4244689 | p.Lys486Thr | missense_variant | 0.17 |
embA | 4245295 | p.Thr688Lys | missense_variant | 0.14 |
embB | 4245905 | c.-609C>A | upstream_gene_variant | 0.4 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.46 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.33 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.33 |
embB | 4246747 | p.Asp78Glu | missense_variant | 0.12 |
embB | 4248534 | p.Ala674Asp | missense_variant | 0.2 |
aftB | 4268832 | p.Val2Ala | missense_variant | 0.2 |
aftB | 4268858 | c.-22G>T | upstream_gene_variant | 0.15 |
ubiA | 4269174 | p.Phe220Leu | missense_variant | 0.25 |
ubiA | 4269345 | c.487_488delGC | frameshift_variant | 0.2 |
aftB | 4269768 | c.-932C>G | upstream_gene_variant | 0.14 |
ethR | 4326961 | c.-588G>C | upstream_gene_variant | 0.22 |
ethR | 4326964 | c.-585G>A | upstream_gene_variant | 0.22 |
ethR | 4326970 | c.-579G>T | upstream_gene_variant | 0.25 |
ethR | 4327738 | p.Tyr64His | missense_variant | 0.13 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |