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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,831,027 C→T 44.5% intergenic (‑98/‑68) ygbI ← / → ygbJ predicted DNA‑binding transcriptional regulator/predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,831,0270CT44.5% 22.3 / 72.3 92intergenic (‑98/‑68)ygbI/ygbJpredicted DNA‑binding transcriptional regulator/predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain
Reads supporting (aligned to +/- strand):  ref base C (27/24);  new base T (28/13);  total (55/37)
Fisher's exact test for biased strand distribution p-value = 1.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 107 total aligned reads displayed.

AACGCTTAGTTCACATAAAATAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAG  >  minE/1830968‑1831094
                                                           |                                                                   
aaCGCTTAGTTCACATAAAATAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCt                                                             >  1:959909/1‑68 (MQ=255)
aaCGCTTAGTTCACATAAAATAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCt                                                             >  1:2808453/1‑68 (MQ=255)
aaCGCTTAGTTCACATAAAATAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCt                                                             >  1:175394/1‑68 (MQ=255)
aaCGCTTAGTTCACATAAAATAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCt                                                             >  1:1676957/1‑68 (MQ=255)
          tCACATAAAATAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTta                                                  <  1:1022803/69‑1 (MQ=255)
          tCACATAAAATAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTta                                                  <  1:355251/69‑1 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:1760436/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:2356693/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:2359981/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:2850640/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:1829509/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:1729326/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:3419960/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:66173/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:363227/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGtt                                                                 >  1:466453/1‑47 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGt                                                                  >  1:2272317/1‑46 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGt                                                                  >  1:70268/1‑46 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTcac                                           <  1:3257892/69‑1 (MQ=255)
                 aaaTAACACACAATGTTAATTTATGTGAATCAGATCACAATACCGtt                                                                 >  1:2786330/1‑47 (MQ=255)
                   aTAACATGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:671087/1‑69 (MQ=255)
                   aTAACACGCAATTTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:2611760/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGt                                                                  >  1:2376553/1‑44 (MQ=25)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTAt                                                               >  1:2410465/1‑47 (MQ=25)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTcaca                                          >  1:2578931/1‑68 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTc                                             >  1:2716316/1‑65 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:837772/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:786713/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:912807/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:2926780/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:2876765/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:2933065/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:3106731/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:3112321/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:3211454/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:2566042/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:394123/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:3243821/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:3260102/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:3295073/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:2233145/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:1897453/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:1098141/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:1526880/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:1871477/1‑69 (MQ=255)
                   aTAACACGCAATGTTAATTTTTGTGAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACaa                                         >  1:1130163/1‑69 (MQ=255)
                   aTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACaa                                         <  1:28907/69‑1 (MQ=255)
                   aTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACaa                                         <  1:1502716/69‑1 (MQ=255)
                   aTAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACaa                                         <  1:633313/69‑1 (MQ=255)
                             aTGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATcaaacaa                               <  1:1086275/69‑1 (MQ=255)
                                ttAATTTATGTGATTCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACaaaa                             >  1:1464250/1‑68 (MQ=255)
                                ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACaaaa                             >  1:510619/1‑68 (MQ=255)
                                ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                            <  1:1950782/69‑1 (MQ=255)
                                ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                            <  1:2878562/69‑1 (MQ=255)
                                ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                            >  1:1719606/1‑69 (MQ=255)
                                ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                            >  1:1784965/1‑69 (MQ=255)
                                ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                            <  1:2484158/69‑1 (MQ=255)
                                ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                            <  1:1660879/69‑1 (MQ=255)
                                    tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                         <  1:2127457/68‑1 (MQ=255)
                                    tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                         <  1:2051324/68‑1 (MQ=255)
                                    tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                         <  1:1413835/68‑1 (MQ=255)
                                    tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                         <  1:2408791/68‑1 (MQ=255)
                                    tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                         <  1:2731427/68‑1 (MQ=255)
                                    tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                         <  1:2658823/68‑1 (MQ=255)
                                    tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                         <  1:1190144/68‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:1500003/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:3384609/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:3012459/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:2951066/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:1971586/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:2906717/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:462841/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:2203001/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:2390032/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:1087442/65‑1 (MQ=255)
                                     ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                        <  1:2247509/65‑1 (MQ=255)
                                                    cACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAg          >  1:2923825/1‑67 (MQ=255)
                                                    cACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAg          >  1:2960712/1‑67 (MQ=255)
                                                    cACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAg          >  1:2836933/1‑67 (MQ=255)
                                                    cACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAg          >  1:2157790/1‑67 (MQ=255)
                                                       cATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGagag     <  1:765359/69‑1 (MQ=255)
                                                          aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  <  1:484685/69‑1 (MQ=255)
                                                          aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  <  1:1042726/69‑1 (MQ=255)
                                                          aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  <  1:2254648/69‑1 (MQ=255)
                                                          aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  <  1:2373285/69‑1 (MQ=255)
                                                          aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  <  1:2230997/69‑1 (MQ=255)
                                                          aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  <  1:2185173/69‑1 (MQ=255)
                                                          aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  <  1:2220560/69‑1 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                            >  1:2079388/1‑42 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:2597391/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  <  1:2258108/68‑1 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:2422156/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:1147332/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:256822/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:341168/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:2170759/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:1372247/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:280161/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:1413907/1‑68 (MQ=255)
                                                           ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg  >  1:3341260/1‑68 (MQ=255)
                                                           |                                                                   
AACGCTTAGTTCACATAAAATAACACACAATGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAG  >  minE/1830968‑1831094

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A