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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,564,912 G→A 22.9% intergenic (‑124/+168) yfdE ← / ← glk predicted CoA‑transferase, NAD(P)‑binding/glucokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,564,9120GA22.9% 168.4 / 46.3 83intergenic (‑124/+168)yfdE/glkpredicted CoA‑transferase, NAD(P)‑binding/glucokinase
Reads supporting (aligned to +/- strand):  ref base G (31/33);  new base A (9/10);  total (40/43)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.36e-01

AAATCAATAACATGATTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAGTGTGACG  >  minE/1564843‑1564982
                                                                     |                                                                      
aaaTCAATAACATGATTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAg                                                                        >  1:3267411/1‑70 (MQ=255)
aaaTCAATAACATGATTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAg                                                                        <  1:785322/70‑1 (MQ=255)
    cAATAACATGATTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACa                                                                    >  1:3189772/1‑70 (MQ=255)
          cATGATTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGcc                                                             <  1:3083108/71‑1 (MQ=255)
              aTTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGa                                                                       >  1:2140398/1‑57 (MQ=255)
              aTTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACa                                                                    <  1:80212/60‑1 (MQ=255)
              aTTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTa                                                         >  1:210882/1‑71 (MQ=255)
               ttAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTa                                                         >  1:2194120/1‑70 (MQ=255)
               ttAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTAc                                                        <  1:3718953/71‑1 (MQ=255)
               ttAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTAc                                                        <  1:3294472/71‑1 (MQ=255)
                tAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTAc                                                        >  1:1799792/1‑70 (MQ=255)
                 atcGTTAATTCCTCGTTGAGTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAATCGCCGTTAc                                                        >  1:3480495/3‑69 (MQ=255)
                 atcGTTAATTCCTCGTTCAGTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAATCGCCGTTAc                                                        >  1:1384860/3‑69 (MQ=255)
                 aaCGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTa                                                         >  1:2785382/1‑68 (MQ=255)
                   cGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGt                                                           >  1:1741778/1‑64 (MQ=255)
                    gTTAATTCCTCGTTCAGTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGa                                                    >  1:2128414/1‑70 (MQ=255)
                     ttAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCg                                                               <  1:3275820/58‑1 (MQ=255)
                      tAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAAt                                                                 >  1:923120/1‑55 (MQ=255)
                      tAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCg                                                               >  1:2621014/1‑57 (MQ=255)
                      tAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGAc                                                   >  1:3735762/1‑69 (MQ=255)
                      tAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACa                                                  >  1:2388169/1‑70 (MQ=255)
                        aTTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGa                                                                       >  1:739047/1‑47 (MQ=255)
                        aTTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACaaa                                                >  1:244856/1‑70 (MQ=255)
                        aTTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACaaa                                                >  1:1020651/1‑70 (MQ=255)
                           ccTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACa                                                  <  1:2502957/65‑1 (MQ=255)
                           ccTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAaataat                                            >  1:3528328/1‑71 (MQ=255)
                           ccTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAaataat                                            >  1:1563598/1‑71 (MQ=255)
                           ccTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAaataat                                            >  1:3975205/1‑71 (MQ=255)
                           ccTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAaata                                              >  1:854223/1‑69 (MQ=255)
                               gTTCAGTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAAt                                                                 >  1:1632440/1‑46 (MQ=255)
                               gTTCAGTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAAt                                                                 >  1:4140118/1‑46 (MQ=255)
                               gTTCAGTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACAAATAATGCa                                         <  1:1234348/70‑1 (MQ=255)
                               gTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACaaa                                                <  1:2041071/63‑1 (MQ=255)
                               gTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGc                                          <  1:3220759/69‑1 (MQ=255)
                                ttCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCAtt                                       <  1:2815245/71‑1 (MQ=255)
                                ttCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCAtt                                       <  1:274194/71‑1 (MQ=255)
                                ttCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCAtt                                       <  1:1079005/71‑1 (MQ=255)
                                  cAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACaaa                                                                  >  1:1643828/1‑42 (MQ=255)
                                  cAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCa                                         >  1:2717678/1‑67 (MQ=255)
                                   aGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTAc                                    <  1:1832566/71‑1 (MQ=255)
                                   aGTAATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTAc                                    <  1:959635/71‑1 (MQ=255)
                                    gTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACAaataat                                            <  1:266261/62‑1 (MQ=255)
                                    gTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACAaataat                                            <  1:2799445/62‑1 (MQ=255)
                                    gTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACAAATAATGCATTTACt                                   >  1:1340844/1‑71 (MQ=255)
                                    gTGATAGTTGACGAGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACAAATAATGCATTTACt                                   >  1:468703/1‑71 (MQ=255)
                                     tGATAGTTGACGAGTGAAATTATGAACGTGCAAAACaa                                                                   <  1:821852/38‑1 (MQ=38)
                                     tGATAGTTGACGAGTGAAATTATGAACGTGCAAAACa                                                                    <  1:190116/37‑1 (MQ=38)
                                     tGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACaaa                                                <  1:2818191/57‑1 (MQ=255)
                                      gATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAAt                                                                 >  1:440689/1‑39 (MQ=255)
                                        tAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGgag                               <  1:148603/71‑1 (MQ=255)
                                          gTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACaaa                                                >  1:865397/1‑52 (MQ=255)
                                           ttgacgaGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACAaat                                               <  1:1262057/50‑1 (MQ=255)
                                           ttgacgaGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAAt                            <  1:2907012/69‑1 (MQ=255)
                                           tCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAAt                            >  1:64638/1‑71 (MQ=255)
                                            cgacgaGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAAt                            >  1:846183/1‑70 (MQ=255)
                                             gacgaGTGAAATTATGAACGTGCAGAACAAATCGCCGt                                                           >  1:2116572/1‑38 (MQ=255)
                                             gacgaGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCa                                                      <  1:2169567/43‑1 (MQ=255)
                                             gacgaGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAaataat                                            <  1:466551/53‑1 (MQ=255)
                                             gacgaGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAAtt                           >  1:1576893/1‑70 (MQ=255)
                                             gacgaGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACaaa                                                >  1:2817539/1‑49 (MQ=255)
                                              acgaGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTaa                         <  1:2276222/71‑1 (MQ=255)
                                               cgaGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAAt                        <  1:3348332/71‑1 (MQ=255)
                                                gaGTGAAATTATGAACGTGCAAAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTaa                         <  1:2627983/69‑1 (MQ=255)
                                                   tGAAATTATGAGCGTGCAGAACAAATCGCCGTTACCAGACAaat                                               <  1:4022230/44‑1 (MQ=255)
                                                   tGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAaat                                               <  1:1446806/44‑1 (MQ=255)
                                                   tGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATg                                           <  1:1292230/48‑1 (MQ=255)
                                                     aaaTTATGAACGTGCAGCACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCt                  >  1:937826/1‑71 (MQ=255)
                                                     aaaTTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGc                                          >  1:1099615/1‑47 (MQ=255)
                                                     aaaTTATGAACGTGCAAAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCt                  >  1:2389662/1‑71 (MQ=255)
                                                      aaTTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTg                 <  1:2296014/71‑1 (MQ=255)
                                                      aaTTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTg                 <  1:1902601/71‑1 (MQ=255)
                                                      aaTTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTg                 <  1:609582/71‑1 (MQ=255)
                                                      aaTTATGAACGTGCAAAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTg                 <  1:1156322/71‑1 (MQ=255)
                                                      aaTTATGAACGTGCAAAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTg                 <  1:1966755/71‑1 (MQ=255)
                                                       aTTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGt                <  1:4065651/71‑1 (MQ=255)
                                                        ttATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGaa                             <  1:4059868/57‑1 (MQ=255)
                                                        ttATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGaa                             <  1:1111483/57‑1 (MQ=255)
                                                        ttATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGaa                             <  1:361840/57‑1 (MQ=255)
                                                         tATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCa                                         >  1:241467/1‑44 (MQ=255)
                                                          aTGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACg             >  1:2032016/1‑71 (MQ=255)
                                                               cGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAgt        <  1:2806066/71‑1 (MQ=255)
                                                                gTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAgtg       <  1:2681702/71‑1 (MQ=255)
                                                                 tGCAGAACAAATCGCCGTTAGCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAgtgt      <  1:3776513/71‑1 (MQ=255)
                                                                 tGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAgtgt      <  1:1910929/71‑1 (MQ=255)
                                                                    aGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAGTGTGAc   >  1:3525406/1‑71 (MQ=255)
                                                                     gAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAGTGTGACg  <  1:1204045/71‑1 (MQ=255)
                                                                     gAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAGTGTGACg  >  1:2146060/1‑71 (MQ=255)
                                                                     gAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAGTGTGACg  <  1:398870/71‑1 (MQ=255)
                                                                     |                                                                      
AAATCAATAACATGATTAACGTTAATTCCTCGTTCAGTGATAGTCGACGAGTGAAATTATGAACGTGCAGAACAAATCGCCGTTACCAGACAAATAATGCATTTACTGGAGAATTAATCCCGCTGTACGGAAGTGTGACG  >  minE/1564843‑1564982

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