Run ID: ERR2229630
Sample name:
Date: 31-03-2023 17:22:36
Number of reads: 586958
Percentage reads mapped: 99.06
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 | 5889 | p.Glu217Val | missense_variant | 0.13 |
gyrB | 6514 | p.Glu425Asp | missense_variant | 0.14 |
gyrB | 6803 | p.Leu522Met | missense_variant | 0.22 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7698 | c.397C>A | synonymous_variant | 0.33 |
gyrA | 7718 | p.Met139Ile | missense_variant | 0.33 |
gyrA | 8125 | p.Pro275Leu | missense_variant | 0.12 |
gyrA | 8721 | p.Arg474Trp | missense_variant | 0.33 |
fgd1 | 490947 | c.165G>A | synonymous_variant | 0.2 |
mshA | 575571 | p.Ser75Ile | missense_variant | 0.2 |
mshA | 575963 | p.Val206Phe | missense_variant | 0.17 |
ccsA | 620137 | p.Val83Phe | missense_variant | 0.4 |
ccsA | 620765 | p.Ala292Asp | missense_variant | 0.14 |
rpoB | 760803 | p.Val333Met | missense_variant | 0.14 |
rpoB | 760862 | c.1056G>T | synonymous_variant | 0.2 |
rpoB | 760869 | p.Val355Phe | missense_variant | 0.18 |
rpoB | 761152 | p.Leu449Gln | missense_variant | 0.22 |
rpoB | 761958 | p.Met718Val | missense_variant | 0.15 |
rpoC | 765124 | c.1755G>T | synonymous_variant | 0.25 |
rpoC | 766852 | p.Met1161Ile | missense_variant | 0.33 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775726 | c.2755C>T | synonymous_variant | 0.17 |
mmpL5 | 775727 | c.2754C>G | synonymous_variant | 0.15 |
mmpL5 | 775914 | p.Ala856Val | missense_variant | 0.25 |
mmpL5 | 775954 | c.2527C>T | synonymous_variant | 0.15 |
mmpL5 | 775957 | p.Ile842Val | missense_variant | 0.15 |
mmpL5 | 775964 | p.Ala839Ser | missense_variant | 0.15 |
mmpL5 | 776514 | p.His656Arg | missense_variant | 0.12 |
mmpL5 | 777119 | p.His454Gln | missense_variant | 0.27 |
mmpL5 | 777122 | c.1359C>T | synonymous_variant | 0.33 |
mmpL5 | 777128 | c.1353A>G | synonymous_variant | 0.33 |
mmpL5 | 777157 | c.1324C>A | synonymous_variant | 0.15 |
mmpL5 | 777164 | c.1317C>T | synonymous_variant | 0.17 |
mmpR5 | 778340 | c.-650G>A | upstream_gene_variant | 0.25 |
mmpL5 | 778913 | c.-433G>T | upstream_gene_variant | 0.2 |
mmpR5 | 779360 | p.Ala124Glu | missense_variant | 0.29 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800902 | p.Gly32Arg | missense_variant | 0.22 |
rplC | 801435 | c.627C>A | synonymous_variant | 0.15 |
fbiC | 1302741 | c.-190G>A | upstream_gene_variant | 0.33 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
Rv1258c | 1406122 | p.Pro407Thr | missense_variant | 0.22 |
Rv1258c | 1406668 | c.673T>C | synonymous_variant | 0.25 |
Rv1258c | 1406926 | p.Leu139Met | missense_variant | 0.18 |
Rv1258c | 1407045 | p.Asp99Gly | missense_variant | 0.25 |
embR | 1416470 | p.His293Pro | missense_variant | 0.2 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472359 | n.514A>G | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472417 | n.572G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.14 |
fabG1 | 1673618 | p.Cys60Tyr | missense_variant | 0.22 |
fabG1 | 1673654 | p.Phe72Ser | missense_variant | 0.22 |
fabG1 | 1673900 | p.Ala154Val | missense_variant | 0.18 |
rpsA | 1833552 | p.Pro4Arg | missense_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918643 | p.Gly235Val | missense_variant | 0.15 |
ndh | 2101819 | p.Lys408Asn | missense_variant | 0.25 |
katG | 2155338 | p.Asn258Lys | missense_variant | 0.25 |
katG | 2155456 | p.Pro219Leu | missense_variant | 0.18 |
katG | 2155990 | p.Asn41Ser | missense_variant | 0.15 |
katG | 2156543 | c.-432G>C | upstream_gene_variant | 0.11 |
PPE35 | 2167686 | p.Asn976Thr | missense_variant | 0.18 |
PPE35 | 2167695 | p.Ile973Thr | missense_variant | 0.22 |
PPE35 | 2167745 | p.Thr956Arg | missense_variant | 0.2 |
PPE35 | 2167814 | c.2799C>T | synonymous_variant | 0.2 |
PPE35 | 2167833 | p.Leu927Arg | missense_variant | 0.18 |
PPE35 | 2167865 | c.2748G>C | synonymous_variant | 0.17 |
PPE35 | 2167868 | c.2745A>C | synonymous_variant | 0.18 |
PPE35 | 2168140 | p.Ala825Thr | missense_variant | 0.2 |
PPE35 | 2168143 | p.Phe824Leu | missense_variant | 0.2 |
PPE35 | 2168150 | c.2463T>C | synonymous_variant | 0.2 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2169141 | p.Thr491Lys | missense_variant | 0.13 |
PPE35 | 2169488 | c.1125G>C | synonymous_variant | 0.14 |
PPE35 | 2169570 | p.Ser348Asn | missense_variant | 0.16 |
PPE35 | 2169602 | c.1011C>A | synonymous_variant | 0.24 |
PPE35 | 2169628 | p.Ile329Val | missense_variant | 0.11 |
PPE35 | 2169629 | c.984T>C | synonymous_variant | 0.11 |
PPE35 | 2169632 | p.Ala327Gly | missense_variant | 0.12 |
PPE35 | 2169638 | c.975T>C | synonymous_variant | 0.13 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.23 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.64 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.66 |
PPE35 | 2170147 | p.Ser156Ala | missense_variant | 0.23 |
Rv1979c | 2222458 | p.Glu236Val | missense_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518809 | p.Lys232Arg | missense_variant | 0.2 |
kasA | 2519052 | p.Thr313Met | missense_variant | 0.18 |
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.38 |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.38 |
eis | 2714448 | p.Trp295Cys | missense_variant | 0.67 |
eis | 2715531 | c.-199C>T | upstream_gene_variant | 0.33 |
pepQ | 2859303 | c.1116G>A | synonymous_variant | 0.18 |
ribD | 2987365 | p.Ala176Glu | missense_variant | 0.17 |
ribD | 2987436 | p.Gly200Trp | missense_variant | 0.18 |
Rv2752c | 3065216 | p.Ile326Val | missense_variant | 0.5 |
Rv2752c | 3065401 | p.Arg264Pro | missense_variant | 0.15 |
thyX | 3067758 | p.His63Leu | missense_variant | 0.22 |
thyA | 3074175 | c.297A>T | synonymous_variant | 0.67 |
thyA | 3074413 | p.Asp20Gly | missense_variant | 0.29 |
ald | 3086640 | c.-180T>A | upstream_gene_variant | 0.4 |
fbiD | 3339588 | c.471G>T | synonymous_variant | 0.25 |
fbiD | 3339645 | c.528C>T | synonymous_variant | 0.29 |
fprA | 3474806 | p.Met267Thr | missense_variant | 0.2 |
fprA | 3475335 | p.Lys443Asn | missense_variant | 0.29 |
Rv3236c | 3612957 | p.Ala54Thr | missense_variant | 0.22 |
fbiB | 3642047 | c.513G>C | synonymous_variant | 0.5 |
fbiB | 3642765 | p.Glu411* | stop_gained | 0.15 |
alr | 3840473 | p.Asp316Glu | missense_variant | 0.2 |
alr | 3840483 | p.Gly313Val | missense_variant | 0.18 |
alr | 3841247 | p.His58Gln | missense_variant | 0.17 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.33 |
alr | 3841612 | c.-193_-192insC | upstream_gene_variant | 0.26 |
rpoA | 3878168 | p.Ala114Thr | missense_variant | 0.33 |
clpC1 | 4038281 | p.Asp808Glu | missense_variant | 0.33 |
clpC1 | 4039645 | p.His354Asp | missense_variant | 0.18 |
clpC1 | 4039654 | p.Thr351Ser | missense_variant | 0.13 |
clpC1 | 4039691 | c.1014G>C | synonymous_variant | 0.13 |
clpC1 | 4039714 | p.Tyr331His | missense_variant | 0.18 |
clpC1 | 4040144 | c.561G>C | synonymous_variant | 0.33 |
embC | 4239864 | c.2T>C | start_lost | 0.18 |
embC | 4240694 | p.Ile278Val | missense_variant | 0.13 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244414 | c.1182G>T | synonymous_variant | 0.22 |
embA | 4246035 | p.Glu935* | stop_gained | 0.29 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.43 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.56 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.56 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.5 |
embB | 4246567 | c.54_55insT | frameshift_variant | 0.25 |
embB | 4246879 | c.366C>A | synonymous_variant | 0.29 |
embB | 4246904 | p.Val131Leu | missense_variant | 0.22 |
embB | 4247426 | p.Gly305Thr | missense_variant | 0.4 |
embB | 4247470 | c.957T>C | synonymous_variant | 0.25 |
embB | 4247472 | p.Phe320Tyr | missense_variant | 0.25 |
embB | 4248055 | c.1542G>T | synonymous_variant | 0.18 |
embB | 4248401 | p.Ala630Ser | missense_variant | 0.14 |
embB | 4248636 | p.Pro708Leu | missense_variant | 0.4 |
embB | 4248862 | c.2349C>T | synonymous_variant | 0.18 |
embB | 4249034 | c.2521C>A | synonymous_variant | 0.25 |
embB | 4249040 | p.Pro843Thr | missense_variant | 0.25 |
embB | 4249088 | p.Val859Phe | missense_variant | 0.18 |
embB | 4249248 | p.Pro912His | missense_variant | 0.25 |
aftB | 4267087 | p.Leu584Met | missense_variant | 0.15 |
aftB | 4267406 | p.Lys477His | missense_variant | 0.18 |
aftB | 4267411 | p.Gly476Cys | missense_variant | 0.18 |
aftB | 4267413 | p.Gly475Ala | missense_variant | 0.18 |
ethA | 4326153 | p.Arg441Ser | missense_variant | 0.17 |
ethA | 4326503 | p.Gly324Val | missense_variant | 0.17 |
ethR | 4327219 | c.-330G>T | upstream_gene_variant | 0.15 |
ethA | 4327257 | p.Gln73Lys | missense_variant | 0.14 |
ethA | 4327614 | c.-141G>C | upstream_gene_variant | 0.12 |
whiB6 | 4338384 | c.138C>T | synonymous_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407732 | c.471G>A | synonymous_variant | 0.2 |
gid | 4408471 | c.-269G>C | upstream_gene_variant | 0.22 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |