mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 64,536 | C→T | V415V (GTG→GTA) | polB ← | DNA polymerase II |
| RA | 64,539 | T→C | S414S (TCA→TCG) | polB ← | DNA polymerase II |
| RA | 64,593 | C→T | P396P (CCG→CCA) | polB ← | DNA polymerase II |
| RA | 64,635 | A→G | H382H (CAT→CAC) | polB ← | DNA polymerase II |
| RA | 64,641 | T→A | R380R (CGA→CGT) | polB ← | DNA polymerase II |
| RA | 64,644 | C→A | P379P (CCG→CCT) | polB ← | DNA polymerase II |
| RA | 64,665 | T→C | A372A (GCA→GCG) | polB ← | DNA polymerase II |
| RA | 64,677 | A→T | G368G (GGT→GGA) | polB ← | DNA polymerase II |
| RA | 64,680 | G→C | G367G (GGC→GGG) | polB ← | DNA polymerase II |
| RA | 64,686 | T→G | R365R (CGA→CGC) | polB ← | DNA polymerase II |
| RA | 64,692 | C→T | V363V (GTG→GTA) | polB ← | DNA polymerase II |
| RA | 64,713 | T→C | A356A (GCA→GCG) | polB ← | DNA polymerase II |
| RA | 64,716 | C→T | R355R (CGG→CGA) | polB ← | DNA polymerase II |
| RA | 64,749 | G→A | H344H (CAC→CAT) | polB ← | DNA polymerase II |
| RA | 64,755 | G→A | I342I (ATC→ATT) | polB ← | DNA polymerase II |
| RA | 64,794 | T→C | A329A (GCA→GCG) | polB ← | DNA polymerase II |
| RA | 65,031 | A→G | N250N (AAT→AAC) | polB ← | DNA polymerase II |
| RA | 65,169 | C→T | L204L (TTG→CTA) | polB ← | DNA polymerase II |
| RA | 65,171 | A→G | L204L (TTG→CTA) | polB ← | DNA polymerase II |
| RA | 65,202 | G→A | F193F (TTC→TTT) | polB ← | DNA polymerase II |
| RA | 65,208 | A→G | L191L (CTT→CTC) | polB ← | DNA polymerase II |
| RA | 65,213 | A→C | S190A (TCG→GCG) | polB ← | DNA polymerase II |
| RA | 65,232 | C→T | P183P (CCG→CCA) | polB ← | DNA polymerase II |
| RA | 65,316 | T→A | I155I (ATA→ATT) | polB ← | DNA polymerase II |
| RA | 65,381 | T→C | T134A (ACT→GCT) | polB ← | DNA polymerase II |
| RA | 65,454 | A→G | R109R (CGT→CGC) | polB ← | DNA polymerase II |
| RA | 65,594 | A→C | F63V (TTT→GTT) | polB ← | DNA polymerase II |
| RA | 65,785 | A→T | intergenic (‑5/+70) | polB ← / ← araD | DNA polymerase II/L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 65,788 | A→T | intergenic (‑8/+67) | polB ← / ← araD | DNA polymerase II/L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 65,811 | G→T | intergenic (‑31/+44) | polB ← / ← araD | DNA polymerase II/L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 65,905 | C→T | D216N (GAT→AAT) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,024 | Δ1 bp | coding (527/696 nt) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,032 | C→T | P173P (CCG→CCA) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,041 | G→A | S170S (TCC→TCT) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,053 | A→G | V166V (GTT→GTC) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,092 | A→G | F153F (TTT→TTC) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,134 | G→A | G139G (GGC→GGT) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,227 | A→G | G108G (GGT→GGC) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,245 | G→A | T102T (ACC→ACT) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,263 | C→T | T96T (ACG→ACA) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,266 | A→G | H95H (CAT→CAC) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,287 | G→C | P88P (CCC→CCG) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,323 | G→A | D76D (GAC→GAT) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,343 | T→C | T70A (ACG→GCG) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,403 | C→T | V50I (GTC→ATC) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,494 | G→A | H19H (CAC→CAT) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 66,518 | T→C | E11E (GAA→GAG) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| RA | 75,938 | T→A | L454L (CTA→CTT) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 75,950 | A→G | S450S (AGT→AGC) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 75,953 | T→C | E449E (GAA→GAG) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 75,966 | 2 bp→TC | coding (1333‑1334/1656 nt) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 75,984 | 2 bp→CT | coding (1315‑1316/1656 nt) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 76,000 | T→C | K434E (AAA→GAA) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 89,754 | T→C | Y41H (TAT→CAT) | mraZ → | DNA‑binding transcriptional repressor MraZ |
| RA | 94,278 | G→A | A371A (GCG→GCA) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 679,349 | Δ8,502 bp | IS5‑mediated | [ybeT]–gltI | [ybeT], ybeU, djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| RA | 803,662 | C→A | L54I (CTT→ATT) | ybhJ → | putative hydratase YbhJ |
| JC JC | 1,290,881 | IS1 (+) +9 bp | coding (640‑648/1014 nt) | rssB → | regulator of RpoS |
| JC JC | 1,293,279 | IS5 (+) +4 bp | intergenic (‑357/‑245) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| JC JC | 1,494,489 | IS5 (–) +4 bp | coding (580‑583/924 nt) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| RA | 1,776,715 | A→T | S377C (AGT→TGT) | ydiF → | putative acetate‑CoA transferase YdiF |
| RA | 1,905,761 | G→A | G25D (GGT→GAT) | mntP → | Mn(2(+)) exporter |
| JC JC | 2,000,811 | IS1 (+) +8 bp | coding (207‑214/552 nt) | fliZ ← | DNA‑binding transcriptional regulator FliZ |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| MC JC | 2,175,883 | Δ5 bp | coding (435‑439/1263 nt) | gatZ ← | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone |
| JC JC | 2,315,674 | IS2 (+) +5 bp | coding (2187‑2191/2673 nt) | rcsD → | RcsD phosphotransferase |
| JC JC | 2,379,830 | IS5 (+) +4 bp | coding (811‑814/1296 nt) | menF ← | isochorismate synthase MenF |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 3,262,484 | IS5 (+) +4 bp | coding (1174‑1177/1209 nt) | tdcD ← | propionate kinase |
| RA | 3,326,889 | A→C | M16R (ATG→AGG) | ftsH ← | ATP‑dependent zinc metalloprotease FtsH |
| RA | 3,350,649 | G→A | noncoding (73/121 nt) | arcZ → | small regulatory RNA ArcZ |
| MC JC | 3,398,017 | 312 bp→68 bp | coding (51‑362/594 nt) | yhdE ← | nucleoside triphosphate pyrophosphatase YhdE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,441,201 | A→G | I5I (ATT→ATC) | paeA ← | putative cadaverine/putrescine exporter |
| RA | 4,542,725 | (T)6→5 | intergenic (+92/‑390) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| JC | 4,639,657 | (TCCGGCGTA)2→1 | coding (642‑650/717 nt) | arcA ← | DNA‑binding transcriptional dual regulator ArcA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 66633 | 74192 | 7560 | 11 [0] | [1] 2 | araA–[thiP] | araA,araB,araC,yabI,thiQ,[thiP] |
| * | * | ÷ | NC_000913 | 74289 | 75922 | 1634 | 2 [0] | [0] 11 | [thiP]–[sgrR] | [thiP],thiB,sroA,[sgrR] |
| * | * | ÷ | NC_000913 | 115654 | 115732 | 79 | 2 [1] | [1] 4 | [hofC]–[hofB] | [hofC],[hofB] |
| * | * | ÷ | NC_000913 | 219951 | 220003 | 53 | 3 [1] | [1] 2 | [rcsF] | [rcsF] |
| * | * | ÷ | NC_000913 | 300081 | 300120 | 40 | 2 [1] | [1] 2 | paoC | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| * | * | ÷ | NC_000913 | 584757 | 584824 | 68 | 3 [0] | [1] 2 | ompT | omptin family outer membrane protease OmpT |
| * | * | ÷ | NC_000913 | 586467 | 586514 | 48 | 2 [1] | [1] 2 | envY | DNA‑binding transcriptional activator EnvY |
| * | * | ÷ | NC_000913 | 822520 | 823153 | 634 | 2 [0] | [0] 2 | clsB | cardiolipin synthase B |
| * | * | ÷ | NC_000913 | 823227 | 823742 | 516 | 2 [0] | [1] 3 | [clsB]–[ybhP] | [clsB],[ybhP] |
| * | * | ÷ | NC_000913 | 1158503 | 1158523 | 21 | 2 [1] | [1] 2 | ptsG | glucose‑specific PTS enzyme IIBC component |
| * | * | ÷ | NC_000913 | 1245349 | 1245394 | 46 | 2 [1] | [1] 2 | ycgY | uncharacterized protein YcgY |
| * | * | ÷ | NC_000913 | 1351136 | 1351212 | 77 | 2 [1] | [1] 3 | fabI/ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| * | * | ÷ | NC_000913 | 1756291 | 1757574 | 1284 | 11 [0] | [1] 3 | [pykF]–[lpp] | [pykF],[lpp] |
| * | * | ÷ | NC_000913 | 1902390 | 1902411 | 22 | 2 [1] | [1] 2 | manX | mannose‑specific PTS enzyme IIAB component |
| * | * | ÷ | NC_000913 | 1922239 | 1922263 | 25 | 2 [1] | [0] 2 | yebW | DUF1482 domain‑containing protein YebW |
| * | * | ÷ | NC_000913 | 1978503–1979268 | 1979336 | 69–834 | 20 [0] | [0] 9 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 1992275 | 1992697 | 423 | 3 [0] | [1] 2 | pgsA | CDP‑diacylglycerol‑‑glycerol‑3‑phosphate 3‑phosphatidyltransferase |
| * | * | ÷ | NC_000913 | 1992778 | 1992814 | 37 | 2 [1] | [0] 2 | pgsA | CDP‑diacylglycerol‑‑glycerol‑3‑phosphate 3‑phosphatidyltransferase |
| * | * | ÷ | NC_000913 | 2259081 | 2259514 | 434 | 21 [0] | [1] 2 | [psuK] | [psuK] |
| * | * | ÷ | NC_000913 | 2259701 | 2272605 | 12905 | 2 [1] | [0] 2 | fruA–[yejA] | fruA,fruK,fruB,setB,yeiW,yeiP,yeiQ,yeiR,lpxT,mepS,pdeN,[yejA] |
| * | * | ÷ | NC_000913 | 2272652 | 2280602 | 7951 | 2 [0] | [0] 13 | [yejA]–rsuA | [yejA],yejB,yejE,yejF,yejG,bcr,rsuA |
| * | * | ÷ | NC_000913 | 2378845 | 2378872 | 28 | 2 [1] | [0] 2 | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase |
| * | * | ÷ | NC_000913 | 2449256 | 2449266 | 11 | 2 [1] | [0] 2 | yfcO | DUF2544 domain‑containing protein YfcO |
| * | * | ÷ | NC_000913 | 2708751 | 2708802 | 52 | 2 [1] | [1] 2 | [rseB]–[rseA] | [rseB],[rseA] |
| * | * | ÷ | NC_000913 | 3046054 | 3046087 | 34 | 2 [1] | [1] 2 | ygfF/gcvP | putative oxidoreductase YgfF/glycine decarboxylase |
| * | * | ÷ | NC_000913 | 3312739 | 3312770 | 32 | 2 [0] | [1] 2 | truB | tRNA pseudouridine(55) synthase |
| * | * | ÷ | NC_000913 | 3401559 | 3403360 | 1802 | 2 [1] | [1] 2 | [csrD] | [csrD] |
| * | * | ÷ | NC_000913 | 3423855–3424228 | 3424452–3424238 | 11–598 | 2 [1] | [1] 2 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3725002 | 3725023 | 22 | 3 [0] | [1] 3 | glyQ | glycine‑‑tRNA ligase subunit alpha |
| * | * | ÷ | NC_000913 | 3781062 | 3781142 | 81 | 2 [1] | [1] 2 | lldD/trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| * | * | ÷ | NC_000913 | 3895480 | 3895498 | 19 | 2 [1] | [1] 2 | adeP | adenine:H(+) symporter |
| * | * | ÷ | NC_000913 | 4038017–4038682 | 4040528–4039396 | 715–2512 | 2 [1] | [1] 2 | [rrlA]–[rrfA] | [rrlA],[rrfA] |
| * | * | ÷ | NC_000913 | 4070452 | 4070522 | 71 | 2 [1] | [1] 2 | [yihS] | [yihS] |
| * | * | ÷ | NC_000913 | 4335819 | 4335839 | 21 | 2 [1] | [1] 2 | adiC | arginine:agmatine antiporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 66632 | 0 (0.000) | 11 (0.960) | 7/300 | 0.3 | 100% | intergenic (‑82/+203) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase AraD/L‑arabinose isomerase |
| ? | NC_000913 | 75923 = | 0 (0.000) | coding (1377/1656 nt) | sgrR | DNA‑binding transcriptional dual regulator SgrR | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 19 (1.770) | 14/280 | 0.0 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 11 (1.020) | 10/280 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1756290 | 0 (0.000) | 11 (0.980) | 6/292 | 0.4 | 100% | coding (593/1413 nt) | pykF | pyruvate kinase 1 |
| ? | NC_000913 | 1757579 = | 0 (0.000) | coding (159/237 nt) | lpp | murein lipoprotein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 11 (1.590) +62 bp |
7/180 | 0.1 | 100% | intergenic (‑305/+16) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| ? | NC_000913 | = 2102943 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1979337 = | 0 (0.000) | 9 (0.770) | 8/304 | 0.2 | 100% | intergenic (‑122/‑416) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2259080 | 0 (0.000) | 21 (1.800) | 18/304 | 0.0 | 100% | coding (217/942 nt) | psuK | putative pseudouridine kinase |
| ? | NC_000913 | 2288919 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2280603 = | 0 (0.000) | 12 (1.030) | 10/304 | 0.1 | 100% | intergenic (‑120/‑29) | rsuA/radD | 16S rRNA pseudouridine(516) synthase/putative DNA repair helicase RadD |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||