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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,224,676 T→C 25.0% F180L (TTT→CTT)  yebU → predicted methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,224,6760TC25.0% 116.1 / 45.1 68F180L (TTT→CTT) yebUpredicted methyltransferase
Reads supporting (aligned to +/- strand):  ref base T (28/23);  new base C (14/3);  total (42/26)
Fisher's exact test for biased strand distribution p-value = 4.99e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.03e-01

AGTGTTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGCTCTGGCGAAGGCGT  >  minE/1224606‑1224743
                                                                      |                                                                   
aGTGTTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCgtgt                                                                     >  1:2613235/1‑71 (MQ=255)
aGTGTTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCgtgt                                                                     >  1:1681875/1‑71 (MQ=255)
aGTGTTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCgtgt                                                                     >  1:1445180/1‑71 (MQ=255)
 gtgtTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGtt                                                                    <  1:1031324/71‑1 (MQ=255)
  tgtTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:2287676/71‑1 (MQ=255)
  tgtTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:3032888/71‑1 (MQ=255)
  tgtTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:602765/71‑1 (MQ=255)
  tgtTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:506410/71‑1 (MQ=255)
   gtTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:2543658/70‑1 (MQ=255)
      aCATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTg                                                               >  1:2498342/1‑71 (MQ=255)
      aCATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTg                                                               >  1:3003632/1‑71 (MQ=255)
      aCATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTg                                                               >  1:3149341/1‑71 (MQ=255)
           ccAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGc                                                           <  1:41837/70‑1 (MQ=255)
           ccAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGc                                                           <  1:1077735/70‑1 (MQ=255)
           ccAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGc                                                           <  1:3259271/70‑1 (MQ=255)
             aaTATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGttt                                                                   <  1:3627223/60‑1 (MQ=255)
             aaTATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGttt                                                                   <  1:1536572/60‑1 (MQ=255)
             aaTATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGttt                                                                   <  1:2865209/60‑1 (MQ=255)
             aaTATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGttt                                                                   <  1:2110719/60‑1 (MQ=255)
                 tCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGttt                                                                   <  1:1282039/56‑1 (MQ=255)
                 tCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGc                                                      >  1:2413649/1‑69 (MQ=255)
                 tCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGc                                                      >  1:4056160/1‑69 (MQ=255)
                 tCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGc                                                      >  1:770337/1‑69 (MQ=255)
                 tCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGc                                                      >  1:1312959/1‑69 (MQ=255)
                 tCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGc                                                      >  1:2437846/1‑69 (MQ=255)
                 tCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGc                                                      >  1:2096016/1‑69 (MQ=255)
                   aGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAg                                                   >  1:946169/1‑70 (MQ=255)
                   aGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAg                                                   >  1:392571/1‑70 (MQ=255)
                   aGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAg                                                   >  1:1709038/1‑70 (MQ=255)
                   aGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAg                                                   >  1:4069687/1‑70 (MQ=255)
                   aGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGa                                                  <  1:2526761/71‑1 (MQ=255)
                        cTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGt                                             <  1:1977360/71‑1 (MQ=255)
                        cTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGt                                             <  1:3881308/71‑1 (MQ=255)
                         tgtgGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGttt                                                                   <  1:771374/48‑1 (MQ=255)
                         tgtgGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGttt                                                                   <  1:2532556/48‑1 (MQ=255)
                         tgtgGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGt                                             <  1:3993653/70‑1 (MQ=255)
                          gtgGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:1451229/47‑1 (MQ=255)
                                tCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGc                                      >  1:3053903/1‑70 (MQ=255)
                                tCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGc                                      >  1:3794699/1‑70 (MQ=255)
                                tCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGc                                      >  1:4009459/1‑70 (MQ=255)
                                   gTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:1051203/38‑1 (MQ=255)
                                   gTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:3794341/38‑1 (MQ=255)
                                   gTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:3586824/38‑1 (MQ=255)
                                   gTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:1408859/38‑1 (MQ=255)
                                   gTAATGTTGCGCTCACACATTTTGATGGCCGCGTGctt                                                                   <  1:3362281/38‑1 (MQ=255)
                                    tAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTg                                                                  <  1:1405714/38‑1 (MQ=255)
                                    tAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTg                                                                  <  1:1799178/38‑1 (MQ=255)
                                     aaTGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCAtttt                                >  1:2912325/1‑71 (MQ=255)
                                     aaTGTTGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCAtttt                                >  1:3677514/1‑71 (MQ=255)
                                     aaTGTTGAGCTCACACATTTTGATGGCCGCGTGCTTgg                                                                 >  1:397750/1‑38 (MQ=37)
                                      aTGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCAtttt                                <  1:848257/70‑1 (MQ=255)
                                      aTGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCAtttt                                <  1:3759541/70‑1 (MQ=255)
                                       tGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGc                              <  1:2048870/71‑1 (MQ=255)
                                       tGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGc                              <  1:2417453/71‑1 (MQ=255)
                                       tGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGc                              <  1:3056542/71‑1 (MQ=255)
                                         ttGCGCTCACACATTTTGATGGCCGCGTGTTTGGt                                                                >  1:1910128/1‑35 (MQ=255)
                                         ttGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTg                            <  1:615697/71‑1 (MQ=255)
                                         ttGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTg                            <  1:1451172/71‑1 (MQ=255)
                                         ttGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGTTCGa                                         >  1:1193410/1‑58 (MQ=255)
                                         ttGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGTTCGa                                         >  1:3942501/1‑58 (MQ=255)
                                         ttGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGTTCGa                                         >  1:1656723/1‑58 (MQ=255)
                                         ttGCGCTCACACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGTTCGa                                         >  1:1614288/1‑58 (MQ=255)
                                         ttGCGCTCACACATTTTGATGGCCGCGTGCTTGGTCCGGCAGTGCCAGAAATGTTCg                                          >  1:3615653/1‑57 (MQ=255)
                                           gcgcTCGCACATTTTGATGGCCGCGTGCTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGa                          >  1:536313/1‑71 (MQ=255)
                                            cgcTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCt                             >  1:3644847/1‑67 (MQ=255)
                                            cgcTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCt                             >  1:4067066/1‑67 (MQ=255)
                                            cgcTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGACAGAAATGTTCGATGCCATTTTGCt                             >  1:1147861/1‑67 (MQ=255)
                                                 acacaTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGa                          >  1:782156/1‑65 (MQ=255)
                                                 acacaTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGa                          >  1:2847720/1‑65 (MQ=255)
                                                 acacaTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGa                          >  1:74718/1‑65 (MQ=255)
                                                 acacaTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGa                          >  1:2375567/1‑65 (MQ=255)
                                                 acacaTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGa                          >  1:3119947/1‑65 (MQ=255)
                                                 acacaTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGa                          >  1:3516578/1‑65 (MQ=255)
                                                 acacaTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCt                      <  1:1656596/69‑1 (MQ=255)
                                                    caTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAAAGTTCGa                                         >  1:315979/1‑47 (MQ=255)
                                                     aTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGc                >  1:1855382/1‑71 (MQ=255)
                                                     aTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGc                >  1:3950808/1‑71 (MQ=255)
                                                     aTTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGc                <  1:1895828/71‑1 (MQ=255)
                                                      ttttGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCg                                          <  1:3430525/44‑1 (MQ=255)
                                                      ttttGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCg                                          <  1:2283483/44‑1 (MQ=255)
                                                      ttttGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCAt                                   <  1:2525914/51‑1 (MQ=255)
                                                        ttGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCAttt                                 >  1:934014/1‑51 (MQ=255)
                                                        ttGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGctct             >  1:1552436/1‑71 (MQ=255)
                                                        ttGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGctct             >  1:572233/1‑71 (MQ=255)
                                                        ttGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGctct             >  1:3473483/1‑71 (MQ=255)
                                                              gCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCAtttt                                <  1:660273/46‑1 (MQ=255)
                                                              gCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCAtttt                                <  1:3356637/46‑1 (MQ=255)
                                                              gCCGCGTGTTTGGTGCGGCAGAGCCAGAAATGTTCGATGCCAtttt                                <  1:929924/46‑1 (MQ=255)
                                                                cgcgTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTg                            <  1:996053/48‑1 (MQ=255)
                                                                 gcgTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTg                               <  1:3813463/44‑1 (MQ=255)
                                                                   gtgtTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGCTCTGGCGAAGGCgt  <  1:101561/71‑1 (MQ=255)
                                                                    tgtTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGCTCTGGCGAAGGCgt  <  1:1179024/70‑1 (MQ=255)
                                                                      |                                                                   
AGTGTTACATGCCAATATCAGCCGCTGTGGTATCAGTAATGTTGCGCTCACACATTTTGATGGCCGCGTGTTTGGTGCGGCAGTGCCAGAAATGTTCGATGCCATTTTGCTGGACGCTCCCTGCTCTGGCGAAGGCGT  >  minE/1224606‑1224743

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