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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,530,398 G→A 31.7% A26T (GCA→ACA)  mutM → formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,530,3980GA31.7% 113.6 / 72.2 82A26T (GCA→ACA) mutMformamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase
Reads supporting (aligned to +/- strand):  ref base G (35/21);  new base A (10/16);  total (45/37)
Fisher's exact test for biased strand distribution p-value = 5.69e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

TTACCCGAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGACCAACCA  >  minE/2530332‑2530466
                                                                  |                                                                    
ttACCCGAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAgt                                                                  >  1:2497750/1‑71 (MQ=255)
ttACCCGAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAgt                                                                  <  1:2973796/71‑1 (MQ=255)
  aCCCGAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAgtgg                                                                >  1:3477723/1‑71 (MQ=255)
  aCCCGAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAgtgg                                                                >  1:3576380/1‑71 (MQ=255)
  aCCCGAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAgtgg                                                                >  1:2108787/1‑71 (MQ=255)
   cccGAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAgtggt                                                               <  1:552539/71‑1 (MQ=255)
      gAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTgcg                                                            >  1:2202053/1‑71 (MQ=255)
      gAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTgcg                                                            >  1:32944/1‑71 (MQ=255)
      gAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTgcg                                                            >  1:750653/1‑71 (MQ=255)
      gAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAGTGGTgcg                                                            >  1:1066829/1‑71 (MQ=255)
       aaGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTgcgc                                                           <  1:470584/71‑1 (MQ=255)
       aaGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTgcgc                                                           <  1:3514933/71‑1 (MQ=255)
        aGTTGAAACCAGCCGCCGCGTCATATAACAGCATCTCGTTGTTGCAACCATTCTTCATGCAGTGGTgcgc                                                           <  1:1801463/70‑1 (MQ=255)
         gTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCaa                                                         >  1:4007178/1‑71 (MQ=255)
         gTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCaa                                                         >  1:2737875/1‑71 (MQ=255)
            gAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACa                                                                    >  1:2820081/1‑57 (MQ=255)
            gAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACa                                                                    >  1:2478916/1‑57 (MQ=255)
             aaaCCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCACCCATTCTTCATGCAGTGGTGCGCAACGGa                                                     >  1:2596548/1‑71 (MQ=255)
             aaaCCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGa                                                     >  1:3997836/1‑71 (MQ=255)
              aaCCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAGTGGTgcgc                                                           <  1:3498619/64‑1 (MQ=255)
              aaCCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAGTGGTgcgc                                                           <  1:3738305/64‑1 (MQ=255)
               aCCAGCCGCCGCGGCATAGAACCTCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCa                                                          <  1:1064689/64‑1 (MQ=255)
               aCCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCa                                                          <  1:1851224/64‑1 (MQ=255)
                ccAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGc                                                  <  1:3613980/71‑1 (MQ=255)
                ccAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACTGACGc                                                  <  1:3187674/71‑1 (MQ=255)
                ccAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGc                                                  <  1:3615511/71‑1 (MQ=255)
                 cAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATg                                                                      <  1:1135030/50‑1 (MQ=255)
                 cAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCt                                                 <  1:2538784/71‑1 (MQ=255)
                                 gAACCGCATCTCGTTGGTGCAACCATTCTTCATACAgtgg                                                                >  1:2801640/1‑40 (MQ=255)
                                   aCCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGttt                                  >  1:260079/1‑68 (MQ=255)
                                   aCCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGttt                                  >  1:2822094/1‑68 (MQ=255)
                                     cGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCagaa                             <  1:1992672/71‑1 (MQ=255)
                                     cGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCagaa                             <  1:1172313/71‑1 (MQ=255)
                                      gCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               >  1:438305/1‑68 (MQ=255)
                                      gCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               >  1:812496/1‑68 (MQ=255)
                                      gCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               >  1:3058828/1‑68 (MQ=255)
                                      gCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               >  1:1244722/1‑68 (MQ=255)
                                      gCATCTCGTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               <  1:1139527/68‑1 (MQ=255)
                                         tctcGTTGTTGCAAGCATTCTTCATGCAGTGGTGCGCAACGGACGCt                                                 <  1:1067393/47‑1 (MQ=255)
                                         tctcGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCt                                                 <  1:3005654/47‑1 (MQ=255)
                                         tctcGTTGGTCCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCt                                                 <  1:86354/47‑1 (MQ=255)
                                           tcGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCagaa                             >  1:3697855/1‑65 (MQ=255)
                                           tcGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCagaa                             >  1:3440964/1‑65 (MQ=255)
                                           tcGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATc                       >  1:1508349/1‑71 (MQ=255)
                                           tcGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATc                       >  1:2856275/1‑71 (MQ=255)
                                           tcGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATc                       >  1:746046/1‑71 (MQ=255)
                                           tcGTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTATCAGAAGAGATc                       >  1:2636527/1‑71 (MQ=255)
                                           acGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCagaa                             >  1:3296777/2‑65 (MQ=255)
                                             gTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGAt                        <  1:140652/68‑1 (MQ=255)
                                             gTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGAt                        <  1:2911841/68‑1 (MQ=255)
                                             gTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGAt                        <  1:3767431/68‑1 (MQ=255)
                                             gTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATc                       <  1:2912198/69‑1 (MQ=255)
                                             gTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATc                       <  1:2247382/69‑1 (MQ=255)
                                             gTTGGTGCAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATc                       <  1:3226004/69‑1 (MQ=255)
                                                    cAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGttt               <  1:435691/70‑1 (MQ=255)
                                                    cAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGttt               <  1:4241000/70‑1 (MQ=255)
                                                    cAACCATTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGttt               <  1:748954/70‑1 (MQ=255)
                                                     aaCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTaa             <  1:2881862/71‑1 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCagaaga                           <  1:2693151/56‑1 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               <  1:1522216/52‑1 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               <  1:803010/52‑1 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               <  1:1969237/52‑1 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               <  1:2389473/52‑1 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCag                               <  1:3161933/52‑1 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAg            >  1:3803878/1‑71 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAg            >  1:323938/1‑71 (MQ=255)
                                                      aCCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAg            >  1:688041/1‑71 (MQ=255)
                                                        cATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGc           >  1:2359781/1‑70 (MQ=255)
                                                        cATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGc           >  1:3822405/1‑70 (MQ=255)
                                                        cATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGc           >  1:2394443/1‑70 (MQ=255)
                                                        cATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGc           >  1:1692397/1‑70 (MQ=255)
                                                        cATACTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGt                 >  1:1923245/1‑64 (MQ=255)
                                                         aTTCTTCATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGa         >  1:1149244/1‑71 (MQ=255)
                                                          ttcttcATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGac        >  1:3334752/1‑71 (MQ=255)
                                                          ttcttcATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGac        >  1:3844271/1‑71 (MQ=255)
                                                           tcttcATACAGTGGTGCGCAACGGACGCTTGGGCTGGCCGGTTTCAGAAGAGATc                       <  1:2425820/55‑1 (MQ=255)
                                                            cttcATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAgagaa                        >  1:287305/1‑52 (MQ=255)
                                                            cttcATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGacc       >  1:4049322/1‑70 (MQ=255)
                                                            cttcATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGacc       >  1:285645/1‑70 (MQ=255)
                                                            cttcATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGacc       >  1:2946017/1‑70 (MQ=255)
                                                            cttcATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGa         >  1:1653575/1‑68 (MQ=255)
                                                              tcATACAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGaccaac    >  1:3768832/1‑71 (MQ=255)
                                                                aTGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGaccaacca  <  1:1784441/71‑1 (MQ=255)
                                                                  |                                                                    
TTACCCGAAGTTGAAACCAGCCGCCGCGGCATAGAACCGCATCTCGTTGGTGCAACCATTCTTCATGCAGTGGTGCGCAACGGACGCTTGCGCTGGCCGGTTTCAGAAGAGATCTACCGTTTAAGCGACCAACCA  >  minE/2530332‑2530466

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A