mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 224,846 | T→C | noncoding (1076/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,885 | T→C | noncoding (1115/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,889 | C→T | noncoding (1119/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,893 | T→A | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,903 | G→A | noncoding (1133/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,906 | C→T | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,910 | 2 bp→GT | noncoding (1140‑1141/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,915 | A→C | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,920 | A→T | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,923 | G→A | noncoding (1153/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,933 | A→G | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,938 | T→C | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,943 | T→C | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,968 | G→A | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,977 | G→C | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,984 | C→T | noncoding (1214/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 224,989 | A→T | noncoding (1219/1542 nt) | rrsH → | 16S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 442,961 | G→A | E471E (GAG→GAA) | thiI → | tRNA uridine 4‑sulfurtransferase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,649,867 | T→G | V25G (GTT→GGT) | ydfD → | Qin prophage; lysis protein |
| RA | 1,802,309 | G→C | P88A (CCG→GCG) | thrS ← | threonine‑‑tRNA ligase |
| RA | 1,863,500 | A→G | T244A (ACC→GCC) | gapA → | glyceraldehyde‑3‑phosphate dehydrogenase A |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,616,162 | C→A | A23A (GCC→GCA) | bepA → | beta‑barrel assembly‑enhancing protease |
| RA | 2,653,971 | T→G | noncoding (117/304 nt) | ryfA → | small regulatory RNA RyfA |
| RA | 2,886,861 | T→C | Y120C (TAT→TGT) | cas3 ← | CRISPR‑associated endonuclease/helicase Cas3 |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,426,967 | T→C | noncoding (67/76 nt) | alaU ← | tRNA‑Ala |
| RA | 3,426,969 | T→A | noncoding (65/76 nt) | alaU ← | tRNA‑Ala |
| RA | 3,426,985 | A→T | noncoding (49/76 nt) | alaU ← | tRNA‑Ala |
| RA | 3,426,996 | G→T | noncoding (38/76 nt) | alaU ← | tRNA‑Ala |
| RA | 3,427,002 | A→G | noncoding (32/76 nt) | alaU ← | tRNA‑Ala |
| RA | 3,427,028 | A→G | noncoding (6/76 nt) | alaU ← | tRNA‑Ala |
| RA | 3,427,034 | A→T | intergenic (‑1/+42) | alaU ← / ← ileU | tRNA‑Ala/tRNA‑Ile |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,768,355 | C→T | S60L (TCA→TTA) | yibG → | tetratricopeptide‑like domain‑containing protein YibG |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,835,418 | T→C | N171S (AAT→AGT) | yicJ ← | putative xyloside transporter YicJ |
| RA | 3,847,546 | C→G | G360A (GGC→GCC) | uhpC ← | inner membrane protein sensing glucose‑6‑phosphate |
| RA | 4,037,198 | A→G | noncoding (58/77 nt) | ileT → | tRNA‑Ile |
| RA | 4,037,207 | C→A | noncoding (67/77 nt) | ileT → | tRNA‑Ile |
| RA | 4,037,213 | T→C | noncoding (73/77 nt) | ileT → | tRNA‑Ile |
| JC | 4,037,218 | 42 bp→30 bp | intergenic (+1/‑1) | ileT → / → alaT | tRNA‑Ile/tRNA‑Ala |
| RA | 4,037,265 | T→C | noncoding (6/76 nt) | alaT → | tRNA‑Ala |
| RA | 4,037,291 | T→C | noncoding (32/76 nt) | alaT → | tRNA‑Ala |
| RA | 4,037,297 | C→A | noncoding (38/76 nt) | alaT → | tRNA‑Ala |
| RA | 4,037,308 | T→A | noncoding (49/76 nt) | alaT → | tRNA‑Ala |
| RA | 4,037,324 | A→T | noncoding (65/76 nt) | alaT → | tRNA‑Ala |
| RA | 4,037,326 | A→G | noncoding (67/76 nt) | alaT → | tRNA‑Ala |
| RA | 4,279,622 | T→G | F382V (TTT→GTT) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 433019 | 433103 | 85 | 5 [4] | [4] 5 | nrdR | NrdR transcriptional repressor |
| * | * | ÷ | NC_000913 | 1196287 | 1211437 | 15151 | 5 [4] | [3] 5 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 1978503 | 1979270 | 768 | 15 [0] | [0] 9 | insB‑5–insA‑5 | insB‑5,insA‑5 |
| * | * | ÷ | NC_000913 | 2818144 | 2818205 | 62 | 5 [3] | [3] 5 | [argY] | [argY] |
| * | * | ÷ | NC_000913 | 3423780–3424523 | 3424523 | 1–744 | 5 [4] | [4] 6 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 781143 | 33 (1.010) | 15 (0.510) +TAAACACTTTTTAAC |
8/246 | 1.7 | 41.7% | noncoding (76/76 nt) | valZ | tRNA‑Val |
| ? | NC_000913 | 2947605 = | 14 (0.430) | intergenic (+32/‑2) | metW/metV | tRNA‑Met/tRNA‑Met | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 21 (0.660) | 19/268 | 0.6 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 11 (0.340) | 9/276 | 1.7 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 14 (0.450) | 13/260 | 1.0 | 100% | intergenic (‑305/+16) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 9 (0.270) | 8/276 | 1.9 | 100% | intergenic (‑56/‑482) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | = 2406535 | 19 (0.580) | 27 (0.820) | 24/276 | 0.3 | 60.7% | coding (107/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA |
| ? | NC_000913 | 2406551 = | 16 (0.490) | coding (91/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA | |||||
| * | ? | NC_000913 | 3363001 = | 52 (1.590) | 46 (1.410) | 30/274 | 0.1 | 64.1% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3427037 | 0 (0.000) | 22 (0.830) +26 bp |
11/224 | 1.0 | 100% | intergenic (‑4/+39) | alaU/ileU | tRNA‑Ala/tRNA‑Ile |
| ? | NC_000913 | 3427076 = | NA (NA) | noncoding (77/77 nt) | ileU | tRNA‑Ile | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 60 (1.830) | 39/276 | 0.0 | 93.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.120) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 32 (0.980) | 10 (0.330) | 8/258 | 1.8 | 31.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 13 (0.420) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 32 (0.980) | 21 (0.690) | 16/258 | 0.7 | 49.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 13 (0.420) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||