Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A6 F11 I4 R1 73 908.3 39027734 99.3% 38754539 136.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
MC JC AE015451_phaM1 3,484,017 Δ244,813 bp [PP_3091 CDS (conserved membrane protein of unknown function)][PP_3294 CDS (Universal stress protein family)] 233 genes

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ AE015451_phaM1 3484017 3728829 244813 1043 [0] [0] 1042 [PP_3091 CDS (conserved membrane protein of unknown function)]–[PP_3294 CDS (Universal stress protein family)] [PP_3091 CDS (conserved membrane protein of unknown function)],PP_3092 CDS (conserved protein of unknown function),PP_3093 CDS (conserved protein of unknown function),PP_3094 CDS (conserved exported protein of unknown function),clpV CDS (Protein ClpV1),PP_3096 CDS (conserved protein of unknown function),PP_3097 CDS (conserved protein of unknown function),PP_3098 CDS (conserved protein of unknown function),puuD CDS (uricase_urate oxidase),PP_3100 CDS (conserved protein of unknown function),PP_5562 CDS (conserved protein of unknown function),PP_5563 CDS (conserved membrane protein of unknown function),PP_5565 CDS (conserved protein of unknown function),PP_5566 CDS (protein of unknown function),PP_5567 CDS (protein of unknown function),PP_5568 CDS (conserved membrane protein of unknown function),PP_5569 CDS (protein of unknown function of phage origin),PP_5571 CDS (conserved protein of unknown function),PP_5572 CDS (protein of unknown function),PP_5573 CDS (protein of unknown function),PP_3102 CDS (conserved protein of unknown function),PP_3103 CDS (conserved protein of unknown function),PP_5574 CDS (conserved protein of unknown function),PP_3104 CDS (conserved protein of unknown function),PP_3105 CDS (conserved membrane protein of unknown function),PP_3106 CDS (conserved protein of unknown function),PP_5575 CDS (conserved protein of unknown function),PP_3107 CDS (conserved protein of unknown function),PP_3108 CDS (Rhs‑related protein),PP_5576 CDS (conserved protein of unknown function),PP_5578 CDS (conserved protein of unknown function),PP_3109 CDS (conserved protein of unknown function),PP_5579 CDS (conserved protein of unknown function),PP_5580 CDS (protein of unknown function),PP_5582 CDS (conserved protein of unknown function),PP_5583 CDS (conserved protein of unknown function),PP_3110 CDS (protein of unknown function),PP_5584 CDS (protein of unknown function),PP_3113 CDS (transposase),PP_3114 CDS (transposase),PP_3115 CDS (transposase),lexA‑II CDS (transcriptional repressor),PP_3117 CDS (putative protein involved in error‑prone processing of DNA lesions),imuB CDS (DNA linked enzyme involved in DNA repair),dnaEB CDS (error‑prone DNA polymerase),yeaE CDS (methylglyoxal reductase),PP_3121 CDS (transcriptional regulator_ LysR family),atoA CDS (acetoacetyl CoA‑transferase (subunit A)),atoB CDS (acetoacetyl CoA‑transferase (subunit B)),PP_3124 CDS (putative short chain fatty acid transporter),PP_3125 CDS (putative transcriptional regulator (Cro_CI family)),PP_5586 CDS (exported protein of unknown function),PP_3126 CDS (putative polysaccharide exported protein),PP_5587 CDS (conserved protein of unknown function),PP_3127 CDS (putative Exopolysaccharide transport protein),PP_3128 CDS (putative Exopolysaccharide biosynthesis_transport protein),galE CDS (UDP‑glucose 4‑epimerase),PP_3130 CDS (conserved exported protein of unknown function),PP_3131 CDS (conserved membrane protein of unknown function),PP_3132 CDS (putative Polysaccharide transporter),PP_5588 CDS (conserved protein of unknown function),PP_3133 CDS (putative Oxidoreductase),PP_3134 CDS (conserved protein of unknown function),PP_3135 CDS (putative Glycosyl transferase),PP_3136 CDS (putative O‑acetyltransferase),PP_3137 CDS (Glycosyl transferase_ group 2 family protein),PP_3138 CDS (VirK domain protein),PP_3139 CDS (Glycosyl transferase_ group 1 family protein),PP_3140 CDS (Glycosyl transferase_ group 2 family protein),PP_3141 CDS (Glycosyl transferase_ WecB_TagA_CpsF family),PP_3142 CDS (putative Sugar transferase),PP_3143 CDS (Transcriptional regulator_ LysR family),tdcG‑III CDS (L‑serine dehydratase),PP_3145 CDS (conserved protein of unknown function),PP_3146 CDS (putative Oxidoreductase),potF‑II CDS (putrescine‑binding periplasmic protein),PP_3148 CDS (putative Glutamine synthetase),PP_3149 CDS (Transcriptional regulator_ AraC family),PP_3150 CDS (conserved protein of unknown function),sad‑II CDS (NAD+‑dependent succinate semialdehyde dehydrogenase),yneJ CDS (putative DNA‑binding transcriptional regulator_ LysR‑type),PP_3153 CDS (conserved exported protein of unknown function),pagL‑II CDS (lipid A 3‑O‑deacylase),PP_3155 CDS (putative Outer membrane ferric siderophore receptor),PP_3156 CDS (Universal stress protein family),PP_3157 CDS (Inositol monophosphatase family protein),PP_3158 CDS (conserved exported protein of unknown function),PP_5589 CDS (protein of unknown function containing Rhs repeat‑associated core domain),benR CDS (BenABC operon transcriptional activator),PP_3160 CDS (conserved protein of unknown function),benA CDS (benzoate 1_2‑dioxygenase subunit alpha),benB CDS (benzoate 1_2‑dioxygenase subunit beta),benC CDS (benzoate 1_2‑dioxygenase electron transfer component),benD CDS (1_6‑dihydroxycyclohexa‑2_4‑diene‑1‑carboxylate dehydrogenase),benK CDS (benzoate MFS transporter),catA‑II CDS (catechol 1_2‑dioxygenase),benE‑II CDS (benzoate transport protein),nicP‑I CDS (porin‑like protein),PP_3169 CDS (conserved membrane protein of unknown function),PP_3170 CDS (Transcriptional regulator_ LysR family),PP_3171 CDS (conserved protein of unknown function),PP_3172 CDS (Group II intron‑encoding maturase),nemA CDS (N‑ethylmaleimide reductase_ FMN‑linked),PP_3174 CDS (putative Oxidoreductase),PP_3175 CDS (putative Dioxygenase_ ferredoxin reductase component),PP_3176 CDS (Major facilitator family transporter),PP_3177 CDS (conserved protein of unknown function),garK CDS (glycerate kinase),PP_3179 CDS (Transcriptional regulator_ LysR family),PP_3180 CDS (Smp‑30_Cgr1 family protein),PP_3181 CDS (Site‑specific recombinase_ phage integrase family),PP_3182 CDS (GGDEF domain protein),PP_3183 CDS (SCO1_SenC family protein_cytochrome c),mcoA CDS (Mn(II) copper oxidase A),PP_mr40 ncRNA (TPP regulatory region),pet CDS (Pet18 protein),PP_3186 CDS (putative Transcriptional activator),codB CDS (Cytosine transporter),PP_3188 CDS (conserved protein of unknown function),codA CDS (cytosine deaminase _ isoguanine deaminase),PP_3190 CDS (Ornithine cyclodeaminase_mu‑crystallin family protein),PP_3191 CDS (putative threonine ammonia‑lyase _ dehydratase),PP_3192 CDS (conserved protein of unknown function),PP_3193 CDS (conserved protein of unknown function),PP_3194 CDS (conserved protein of unknown function),PP_3195 CDS (conserved protein of unknown function),PP_3196 CDS (Nodulation protein d1),PP_3197 CDS (Glyoxalase family protein),PP_3198 CDS (Ferredoxin_ 2Fe‑2S),PP_3199 CDS (putative Monooxygenase),PP_3200 CDS (conserved exported protein of unknown function),PP_5590 CDS (conserved exported protein of unknown function),PP_3201 CDS (BNR domain protein),PP_3202 CDS (putative Transporter),PP_3203 CDS (Major facilitator family transporter),PP_3204 CDS (conserved protein of unknown function),PP_3205 CDS (Fumarylacetoacetate hydrolase family protein),PP_3206 CDS (conserved protein of unknown function),PP_3207 CDS (putative Cyclase),PP_3208 CDS (Oxidoreductase_ Pdr_VanB family),PP_3209 CDS (Isoxanthopterin deaminase),PP_3210 CDS (ABC transporter_ permease protein),PP_3211 CDS (ABC transporter_ ATP‑binding protein),PP_3212 CDS (Rieske 2Fe‑2S family protein),PP_3213 CDS (ABC transporter_ periplasmic binding component‑related protein),PP_3214 CDS (conserved exported protein of unknown function),PP_3216 CDS (putative cysteine dioxygenase),PP_3217 CDS (putative Periplasmic aliphatic sulfonate‑binding protein),PP_3218 CDS (Monooxygenase_ NtaA_SnaA_SoxA family),PP_3219 CDS (putative Alkansulfonate monooxygenase),PP_3220 CDS (ABC transporter_ ATP‑binding protein),PP_3221 CDS (ABC transporter_ permease protein),PP_3222 CDS (ABC transporter_ permease protein),PP_3223 CDS (ABC transporter_ periplasmic binding protein),PP_3224 CDS (Class II aldolase_adducin domain protein),PP_3225 CDS (D‑isomer specific 2‑hydroxyacid dehydrogenase family protein),PP_3226 CDS (Acyl‑CoA dehydrogenase‑related protein),PP_3227 CDS (Transcriptional regulator_ LysR family),PP_3228 CDS (putative Periplasmic aliphatic sulfonate‑binding protein),PP_3229 CDS (putative Periplasmic aliphatic sulfonate‑binding protein),PP_3230 CDS (Phosphoribosyl transferase domain protein),PP_3231 CDS (conserved protein of unknown function),PP_3232 CDS (Acetyltransferase_ GNAT family),fnrB CDS (transcriptional regulator with 4Fe‑4S cluster_ Crp_Fnr family),PP_5591 CDS (conserved protein of unknown function),PP_3234 CDS (Heat shock protein_ HSP20 family),PP_3235 CDS (conserved protein of unknown function),PP_3236 CDS (putative Lipoprotein OprI),PP_3237 CDS (Universal stress protein family),PP_3238 CDS (putative Transcriptional regulator PyrR),tnpT‑II CDS (putative cointegrate resolution protein T Tn4652),PP_3240 CDS (conserved protein of unknown function),PP_5592 CDS (conserved protein of unknown function),PP_3241 CDS (conserved exported protein of unknown function),PP_3242 CDS (GGDEF domain protein),PP_3243 CDS (Acetyltransferase_ GNAT family),mgtC CDS (Magnesium transporter_ MgtC family),PP_3245 CDS (conserved protein of unknown function),crtZ CDS (Beta‑carotene hydroxylase),PP_3247 CDS (Transporter_ bile acid_Na+ symporter family),PP_3248 CDS (Dyp‑type peroxidase family protein),PP_3249 CDS (putative oxidoreductase),PP_3250 CDS (putative Transporter),PP_5593 CDS (conserved protein of unknown function),PP_5594 CDS (conserved protein of unknown function),PP_3251 CDS (conserved protein of unknown function),PP_3252 CDS (Modification methylase_ HemK family),PP_3253 CDS (Carboxylate‑amine ligase PP_3253),PP_3254 CDS (putative Nucleosidase),PP_3255 CDS (non‑homologous end joining protein),PP_3256 CDS (Glycosyl transferase_ group 2 family protein),PP_3257 CDS (putative Methyltransferase),PP_3258 CDS (conserved protein of unknown function),PP_3259 CDS (Acyl‑CoA dehydrogenase‑related protein),ligD CDS (DNA ligase D),PP_3261 CDS (conserved protein of unknown function),PP_3262 CDS (putative Metallothionein),PP_5595 CDS (conserved exported protein of unknown function),ybhN CDS (phospholipid modification enzyme),clsB CDS (cardiolipin synthase 2),ybhP‑I CDS (putative phosphohydrolase of unknown function),PP_3266 CDS (conserved protein of unknown function),PP_3267 CDS (putative Clp protease),PP_3268 CDS (MutT_nudix family protein),PP_3269 CDS (conserved protein of unknown function),PP_5596 CDS (conserved protein of unknown function),PP_5597 CDS (conserved protein of unknown function),paaZ CDS (oxepin‑CoA hydrolase_3‑oxo‑5_6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase),phaK CDS (phenylacetic acid‑specific porin),actP‑III CDS (acetate permease),PP_3273 CDS (conserved protein of unknown function),paaE CDS (ring 1_2‑phenylacetyl‑CoA epoxidase_ reductase subunit),paaD CDS (putative subunit of phenylacetate degradation enzyme),paaC CDS (ring 1_2‑phenylacetyl‑CoA epoxidase beta subunit),paaB CDS (ring 1_2‑phenylacetyl‑CoA epoxidase regulatory subunit),paaA CDS (ring 1_2‑phenylacetyl‑CoA epoxidase alpha subunit),paaK CDS (phenylacetate‑CoA ligase),paaJ CDS (3‑oxoadipyl‑CoA_3‑oxo‑5_6‑dehydrosuberyl‑CoA thiolase),paaI CDS (hydroxyphenylacetyl‑CoA thioesterase),paaH CDS (3‑hydroxyadipyl‑CoA dehydrogenase),paaG CDS (1_2‑epoxyphenylacetyl‑CoA isomerase),paaF CDS (enoyl‑CoA hydratase‑isomerase),paaY CDS (detoxifying thioesterase of the phenylacetate degradation pathway),paaX CDS (DNA‑binding transcriptional repressor PaaX(phenylacetyl‑CoA)),fnrC CDS (transcriptional regulator with 4Fe‑4S cluster; Crp_Fnr family),PP_5598 CDS (conserved protein of unknown function),PP_3288 CDS (Universal stress protein family),PP_3289 CDS (Acetyltransferase_ GNAT family),PP_3290 CDS (Universal stress protein family),PP_3291 CDS (Metallo‑beta‑lactamase family protein),PP_3292 CDS (conserved membrane protein of unknown function),PP_3293 CDS (conserved membrane protein of unknown function),[PP_3294 CDS (Universal stress protein family)]

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? AE015451_phaM1 = 34840160 (0.000)916 (1.020) 117/266 0.4 100% coding (1908/3804 nt) PP_3091 CDS (conserved membrane protein of unknown function)
?AE015451_phaM1 3728830 = 0 (0.000)coding (701/891 nt) PP_3294 CDS (Universal stress protein family)

GATK/CNVnator alignment

N/A