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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 | freq | annotation | gene | description |
RA | 84,962 | G→A | 9.1% | A150T (GCC→ACC) | cra → | transcriptional repressor‑activator for carbon metabolism |
RA | 227,132 | C→A | 20.9% | A79A (GCG→GCT) | yafC ← | LysR family putative transcriptional regulator |
JC | 481,304 | +CATCCAC | 100% | coding (88/648 nt) | acrR → | transcriptional repressor |
RA | 663,136 | A→G | 8.0% | S180P (TCG→CCG) | mrdA ← | transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2) |
RA | 982,290 | Δ1 bp | 100% | coding (149/1089 nt) | ompF ← | outer membrane porin 1a (Ia;b;F) |
RA | 1,428,899 | G→A | 100% | intergenic (‑418/+316) | ynaE ← / ← ttcC | cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related |
RA | 1,602,426 | Δ1 bp | 22.7% | coding (854/915 nt) | yneE ← | bestrophin family putative inner membrane protein |
RA | 1,602,427 | Δ1 bp | 23.3% | coding (853/915 nt) | yneE ← | bestrophin family putative inner membrane protein |
RA | 1,607,154 | C→T | 12.4% | G119S (GGT→AGT) | glsB ← | glutaminase 2 |
RA | 1,616,797 | G→T | 12.6% | intergenic (+21/‑106) | ydeE → / → yneM | putative transporter/inner membrane‑associated protein |
RA | 1,737,690 | Δ1 bp | 30.6% | intergenic (‑191/‑24) | ribC ← / → mdtK | riboflavin synthase, alpha subunit/multidrug efflux system transporter |
JC | 2,305,823 | +GGTGTC | 24.4% | coding (406/1104 nt) | ompC ← | outer membrane porin protein C |
RA | 2,332,659 | C→A | 100% | G81C (GGT→TGT) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
RA | 2,333,563 | G→A | 10.0% | G173D (GGT→GAT) | ubiG → | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase |
RA | 2,913,718 | G→T | 7.2% | P130T (CCG→ACG) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
RA | 3,010,197:1 | +G | 100% | coding (779/3099 nt) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
RA | 3,167,383 | G→A | 100% | S458L (TCG→TTG) | parE ← | DNA topoisomerase IV, subunit B |
JC | 3,208,014 | +CCGAAAGCCTGCGTG | 48.7% | coding (1609/1842 nt) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
RA | 3,638,574 | G→A | 5.9% | intergenic (‑32/‑171) | prlC ← / → rlmJ | oligopeptidase A/23S rRNA m(6)A2030 methyltransferase, SAM‑dependent |
RA | 3,678,601 | C→A | 7.6% | S126S (TCG→TCT) | yhjK ← | cyclic‑di‑GMP phosphodiesterase |
RA | 3,872,086 | T→C | 100% | Q465R (CAG→CGG) | gyrB ← | DNA gyrase, subunit B |
RA | 3,872,761 | A→G | 7.4% | I240T (ATC→ACC) | gyrB ← | DNA gyrase, subunit B |
RA | 3,877,753 | G→A | 6.7% | A20T (GCT→ACT) | rpmH → | 50S ribosomal subunit protein L34 |
RA | 4,234,832 | C→T | 8.0% | A58T (GCC→ACC) | malF ← | maltose transporter subunit |
RA | 4,267,384 | Δ1 bp | 100% | intergenic (‑73/‑13) | soxS ← / → soxR | superoxide response regulon transcriptional activator; autoregulator/redox‑sensitive transcriptional activator of soxS; autorepressor |
RA | 4,441,503 | A→G | 7.1% | Q210R (CAG→CGG) | ytfR → | putative ABC superfamily sugar transporter ATP‑binding subunit |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | CP009273 | 380411 | 380485 | 75 | 7 [4] | [3] 6 | yaiS/tauA | putative PIG‑L family deacetylase/taurine transporter subunit |
* | * | ÷ | CP009273 | 579513 | 579587 | 75 | 8 [5] | [5] 6 | appY | global transcriptional activator; DLP12 prophage |
* | * | ÷ | CP009273 | 716364 | 716527 | 164 | 8 [5] | [4] 9 | [kdpE] | [kdpE] |
* | * | ÷ | CP009273 | 731799 | 731880–731868 | 70–82 | 6 [5] | [5] 6 | ybfC/ybfQ | putative periplasmic protein/pseudogene, H repeat‑associated protein |
* | * | ÷ | CP009273 | 766290 | 766346 | 57 | 6 [5] | [3] 6 | mngB/cydA | alpha‑mannosidase/cytochrome d terminal oxidase, subunit I |
* | * | ÷ | CP009273 | 950048 | 950253 | 206 | 8 [5] | [5] 6 | focA/ycaO | formate channel/ribosomal protein S12 methylthiotransferase accessory factor |
* | * | ÷ | CP009273 | 993036 | 993260 | 225 | 6 [5] | [4] 6 | ssuE/elfA | NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit |
* | * | ÷ | CP009273 | 1193141 | 1193258 | 118 | 6 [5] | [3] 9 | ymfE | e14 prophage; putative inner membrane protein |
* | * | ÷ | CP009273 | 1193847 | 1193935–1193911 | 65–89 | 6 [5] | [5] 6 | ymfE/lit | e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression |
* | * | ÷ | CP009273 | 1207125 | 1207167 | 43 | 6 [4] | [4] 6 | [iraM] | [iraM] |
* | * | ÷ | CP009273 | 1207523 | 1207602 | 80 | 6 [3] | [5] 6 | iraM/ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
* | * | ÷ | CP009273 | 1225848 | 1226006 | 159 | 6 [3] | [5] 6 | [hlyE] | [hlyE] |
* | * | ÷ | CP009273 | 1540206 | 1540501 | 296 | 7 [5] | [5] 6 | [yddL] | [yddL] |
* | * | ÷ | CP009273 | 1592506 | 1592612 | 107 | 6 [5] | [5] 6 | yneO/lsrK | pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase |
* | * | ÷ | CP009273 | 1634945 | 1635033 | 89 | 6 [4] | [3] 6 | essQ/cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock protein |
* | * | ÷ | CP009273 | 1980120 | 1980230 | 111 | 6 [5] | [5] 6 | araF/ftnB | L‑arabinose transporter subunit/ferritin B, putative ferrous iron reservoir |
* | * | ÷ | CP009273 | 2185796 | 2185959 | 164 | 8 [4] | [5] 6 | yehD/yehE | putative fimbrial‑like adhesin protein/DUF2574 family protein |
* | * | ÷ | CP009273 | 2456685 | 2456723 | 39 | 6 [5] | [5] 6 | yfdF | uncharacterized protein |
* | * | ÷ | CP009273 | 2462618 | 2462687 | 70 | 7 [5] | [4] 6 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
* | * | ÷ | CP009273 | 2898912 | 2899059 | 148 | 6 [5] | [5] 6 | yqcG | yqcG |
* | * | ÷ | CP009273 | 3576412 | 3576499 | 88 | 6 [5] | [5] 6 | yrhA | pseudogene, interrupted by IS1E |
* | * | ÷ | CP009273 | 4258831 | 4258865 | 35 | 6 [4] | [3] 6 | yjbS | uncharacterized protein |
* | * | ÷ | CP009273 | 4561727 | 4561819 | 93 | 6 [5] | [5] 7 | [yjiS] | [yjiS] |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | CP009273 | 360104 = | 32 (0.910) | 37 (1.050) | 30/274 | NT | 52.9% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
? | CP009273 | = 360286 | 34 (0.960) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
* | ? | CP009273 | 1203246 = | 0 (0.000) | 28 (0.900) | 26/242 | NT | 100% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | 1205075 = | 0 (0.000) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | CP009273 | = 1203261 | 0 (0.000) | 25 (0.800) | 20/242 | NT | 100% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | = 1205058 | 0 (0.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | CP009273 | = 1603336 | 20 (0.570) | 8 (0.230) | 8/274 | NT | 33.3% | intergenic (‑57/+150) | yneE/uxaB | bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent |
? | CP009273 | 1605114 = | 12 (0.340) | intergenic (‑177/+50) | uxaB/yneF | altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase | |||||
* | ? | CP009273 | 1721915 = | 30 (0.850) | 49 (1.390) | 35/274 | NT | 59.8% | coding (1000/1098 nt) | nemA | chromate reductase, quinone reductase, FMN‑linked; N‑Ethylmaleimide reductase; old yellow enzyme |
? | CP009273 | = 1740277 | 36 (1.020) | coding (108/1257 nt) | ydhQ | autotransporter adhesin‑related protein |