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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Marginal read alignment evidence (highest frequency 20 of 26 shown, sorted by frequency from high to low) | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | AP012306 | 1,091,992 | 0 | T | G | 35.0% | 577.1 / 64.1 | 286 | intergenic (+38/‑145) | narI/ychS | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/predicted protein |
* | AP012306 | 341,377 | 0 | T | G | 34.9% | 178.6 / 15.7 | 109 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidin e deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
* | AP012306 | 1,421,147 | 0 | T | G | 30.3% | 458.7 / 15.2 | 231 | T79P (ACC→CCC) | ydhB | predicted DNA‑binding transcriptional regulator |
* | AP012306 | 644,417 | 0 | G | A | 29.1% | 851.4 / inf | 516 | intergenic (+32/‑401) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A |
* | AP012306 | 1,854,851 | 0 | A | C | 28.7% | 543.0 / 71.9 | 240 | T25P (ACC→CCC) | yejH | predicted ATP‑dependet helicase |
* | AP012306 | 257,137 | 0 | T | G | 27.6% | 360.4 / 12.8 | 174 | L496V (TTG→GTG) | betT | choline transporter of high affinity |
* | AP012306 | 1,944,288 | 0 | A | C | 27.5% | 532.0 / 28.3 | 222 | G361G (GGT→GGG) | menE | o‑succinylbenzoate‑CoA ligase |
* | AP012306 | 3,938,887 | 0 | C | T | 25.3% | 537.3 / 128.3 | 249 | S44F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator |
* | AP012306 | 800,675 | 0 | A | C | 24.6% | 643.2 / 26.2 | 256 | T192P (ACC→CCC) | lolA | chaperone for lipoproteins |
* | AP012306 | 3,527,368 | 0 | A | C | 24.6% | 594.1 / 52.3 | 242 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator, L‑rhamnose‑binding |
* | AP012306 | 3,182,861 | 0 | A | C | 24.6% | 287.7 / 18.9 | 114 | L198F (TTA→TTC) | yiaN | predicted transporter |
* | AP012306 | 2,758,909 | 0 | T | G | 24.0% | 648.4 / 17.8 | 242 | G33G (GGT→GGG) | agaD | N‑acetylgalactosamine‑specific enzyme IID component of PTS |
* | AP012306 | 3,903,791 | 0 | A | G | 23.5% | 539.7 / 67.3 | 230 | E189G (GAA→GGA) | yjgJ | predicted transcriptional regulator |
* | AP012306 | 3,639,040 | 0 | T | G | 22.9% | 130.7 / 17.0 | 61 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
* | AP012306 | 472,868 | 0 | T | G | 22.4% | 546.4 / 22.6 | 205 | D435A (GAC→GCC) | cusS | sensory histidine kinase in two‑component regulatory system with CusR, senses copper ions |
* | AP012306 | 2,558,071 | 0 | A | C | 22.3% | 609.1 / 31.9 | 238 | V302G (GTA→GGA) | visC | predicted oxidoreductase, FAD/NAD(P)‑binding domain |
* | AP012306 | 202,417 | 0 | T | G | 21.7% | 724.9 / 22.9 | 269 | V409G (GTA→GGA) | tilS | tRNA(Ile)‑lysidine synthetase |
* | AP012306 | 2,499,414 | 0 | A | C | 21.6% | 804.7 / 62.1 | 301 | P126P (CCA→CCC) | yqeI | predicted transcriptional regulator |
* | AP012306 | 1,226,557 | 0 | A | G | 21.5% | 497.1 / 74.7 | 200 | G55G (GGA→GGG) | ydcU | predicted spermidine/putrescine transporter subunit |
* | AP012306 | 1,128,412 | 0 | T | G | 20.9% | 631.6 / 42.0 | 235 | V29G (GTG→GGG) | yciO | conserved protein |
Marginal new junction evidence (lowest skew 10 of 29 shown) | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | AP012306 | = 997497 | 287 (0.900) | 14 (0.050) | 14/268 | 17.0 | 5.3% | coding (41/1305 nt) | ndh | respiratory NADH dehydrogenase 2/cupric reductase |
? | AP012306 | 997993 = | 241 (0.840) | coding (537/1305 nt) | ndh | respiratory NADH dehydrogenase 2/cupric reductase | |||||
* | ? | AP012306 | = 1092512 | 376 (1.180) | 12 (0.040) | 8/258 | 19.4 | 4.1% | intergenic (+100/+3) | ychS/tpr | predicted protein/predicted protamine‑like protein |
? | AP012306 | 1092985 = | 239 (0.870) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
* | ? | AP012306 | 3838276 = | 450 (1.420) | 6 (0.020) | 6/268 | 20.9 | 1.4% | intergenic (+79/‑101) | rnr/rlmB | exoribonuclease R, RNase R/23S rRNA (Gm2251)‑methyltransferase |
? | AP012306 | 3838337 = | 432 (1.510) | intergenic (+140/‑40) | rnr/rlmB | exoribonuclease R, RNase R/23S rRNA (Gm2251)‑methyltransferase | |||||
* | ? | AP012306 | = 2275071 | 209 (0.660) | 36 (0.130) +GTATCAGTCTGCTTCGCAAG |
5/258 | 21.2 | 13.2% | noncoding (1/76 nt) | gltW | tRNA‑Glu |
? | AP012306 | = 3597478 | 339 (1.070) | intergenic (+65/‑107) | rrsB/gltT | 16S ribosomal RNA (rrnB)/tRNA‑Glu | |||||
* | ? | AP012306 | = 1092334 | 315 (0.990) | 6 (0.020) | 5/258 | 21.2 | 2.3% | coding (198/276 nt) | ychS | predicted protein |
? | AP012306 | 1092985 = | 239 (0.870) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
* | ? | AP012306 | = 2252778 | 404 (1.270) | 6 (0.020) | 6/292 | 21.6 | 1.5% | intergenic (‑27/+171) | lepA/rseC | GTP binding membrane protein/RseC protein |
? | AP012306 | = 2252788 | 410 (1.320) | intergenic (‑37/+161) | lepA/rseC | GTP binding membrane protein/RseC protein | |||||
* | ? | AP012306 | = 2382041 | 281 (0.890) | 6 (0.020) | 6/294 | 21.7 | 2.1% | coding (275/480 nt) | ispF | 2C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase |
? | AP012306 | = 2382058 | 290 (0.930) | coding (258/480 nt) | ispF | 2C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase | |||||
* | ? | AP012306 | = 215364 | NA (NA) | 5 (0.020) | 5/288 | 22.1 | NA | noncoding (745/2905 nt) | rrlH | 23S ribosomal RNA (rrlH) |
? | AP012306 | = 215372 | NA (NA) | noncoding (753/2905 nt) | rrlH | 23S ribosomal RNA (rrlH) | |||||
* | ? | AP012306 | = 3540501 | 281 (0.890) | 4 (0.010) | 4/274 | 22.4 | 1.5% | coding (220/768 nt) | tpiA | triosephosphate isomerase |
? | AP012306 | = 3540489 | 255 (0.870) | coding (232/768 nt) | tpiA | triosephosphate isomerase | |||||
* | ? | AP012306 | = 2947811 | 264 (0.830) | 4 (0.010) | 4/274 | 22.4 | 1.6% | coding (1875/2544 nt) | nirB | nitrite reductase, large subunit, NAD(P)H‑binding |
? | AP012306 | = 2947799 | 254 (0.870) | coding (1863/2544 nt) | nirB | nitrite reductase, large subunit, NAD(P)H‑binding |