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 1,484,894 T→C 22.2% M316V (ATG→GTG)  menF ← isochorismate synthase 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,484,8940TC22.2% 102.7 / 28.9 54M316V (ATG→GTG) menFisochorismate synthase 2
Reads supporting (aligned to +/- strand):  ref base T (22/20);  new base C (7/5);  total (29/25)
Fisher's exact test for biased strand distribution p-value = 7.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01

ACTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGA  >  minE/1484825‑1484961
                                                                     |                                                                   
aCTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCAt                                                                     <  1:4125802/70‑1 (MQ=255)
   gATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTa                                                                 >  1:3920078/1‑71 (MQ=255)
    aTGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCAtttt                                                                  <  1:988674/69‑1 (MQ=255)
    aTGTAAACACATCACTTCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCActtt                                                                  <  1:1964001/69‑1 (MQ=255)
      gTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacg                                                               >  1:587852/1‑70 (MQ=255)
       tAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgca                                                             <  1:2835307/71‑1 (MQ=255)
       tAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacg                                                               >  1:109532/1‑69 (MQ=255)
           cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacg                                                         <  1:3780342/71‑1 (MQ=255)
               tCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGt                                                     <  1:2889075/71‑1 (MQ=255)
                cacaTCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTa                                                                 >  1:884511/1‑58 (MQ=255)
                 acaTCATCCGCTTTGTTGAATGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTa                                                    <  1:458050/70‑1 (MQ=255)
                  catcatACGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacgc                                                        >  1:531689/1‑65 (MQ=255)
                   atcatcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcaga                                                           >  1:2374057/1‑61 (MQ=255)
                    tcatcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGt                                                     <  1:2560830/66‑1 (MQ=255)
                      atcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcaga                                                           >  1:3058541/1‑58 (MQ=255)
                      atcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTa                                                                 >  1:3945309/1‑52 (MQ=255)
                         cGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTgcggcg                                           <  1:2198740/71‑1 (MQ=255)
                         cGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacg                                                         >  1:3045932/1‑57 (MQ=255)
                          gCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacgcag                                                      <  1:2714196/59‑1 (MQ=255)
                           cTTTGTTGAGTGAAGTCCATATACAGCGGCGAAGATGCTGCAtttt                                                                  <  1:891746/46‑1 (MQ=255)
                           cTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCAtttt                                                                  <  1:1995473/46‑1 (MQ=255)
                           cTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGt                                         <  1:1711830/71‑1 (MQ=255)
                              tgttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcaga                                                           >  1:268453/1‑50 (MQ=255)
                              tgttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcaga                                                           >  1:580843/1‑50 (MQ=255)
                              tgttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTaa                                       >  1:2869665/1‑70 (MQ=255)
                              tgttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTaa                                       <  1:551547/70‑1 (MQ=255)
                                ttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacg                                                         <  1:1200711/50‑1 (MQ=255)
                                ttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTAcc                                                  >  1:858957/1‑57 (MQ=255)
                                ttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTAcc                                                  >  1:2446020/1‑57 (MQ=255)
                                    gTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTg                                                >  1:940560/1‑55 (MQ=255)
                                       aaGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgca                                                             >  1:2502995/1‑39 (MQ=255)
                                       aaGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAg                              >  1:3889515/1‑70 (MQ=255)
                                       aaGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGc                             >  1:2494815/1‑71 (MQ=255)
                                         gTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTgc                                               <  1:784465/51‑1 (MQ=255)
                                          tCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTc                          <  1:2946138/71‑1 (MQ=255)
                                            cAGATACAGCGGCGAAGATGCTGCATTTTacgcagacgc                                                        <  1:1084275/39‑1 (MQ=255)
                                            cAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTg                        >  1:151591/1‑71 (MQ=255)
                                            cAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTg                        >  1:1229938/1‑71 (MQ=255)
                                              gATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGt                                         >  1:835101/1‑52 (MQ=255)
                                              gATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTggg                      <  1:3579725/71‑1 (MQ=255)
                                              gATACAGCGGCGAAGATGCTGCACTTTacgcagacg                                                         <  1:3604037/36‑1 (MQ=255)
                                              gATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTggg                      <  1:2500843/71‑1 (MQ=255)
                                               aTACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGt                     <  1:3266683/71‑1 (MQ=255)
                                                 aCAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTa                    >  1:550112/1‑70 (MQ=255)
                                                  cAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGt                     <  1:3264363/68‑1 (MQ=255)
                                                    gcggcgAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCgg                >  1:260274/1‑71 (MQ=255)
                                                         gAAGATGCTGCATTTTACGCAAACGCAGTACCTGCGGCGGTaaaa                                     >  1:2781186/1‑45 (MQ=255)
                                                          aaGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTa          <  1:3071101/71‑1 (MQ=255)
                                                          aaGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTa          <  1:2878986/71‑1 (MQ=255)
                                                            gATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAAt        >  1:2630027/1‑71 (MQ=255)
                                                                ctgcATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGtt    <  1:3288285/71‑1 (MQ=255)
                                                                 tgcATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTg                        <  1:3948279/50‑1 (MQ=255)
                                                                 tgcATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGt                     <  1:3245297/53‑1 (MQ=255)
                                                                 tgcATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCt             <  1:3274777/61‑1 (MQ=255)
                                                                 tgcATTTTACGCAGAAGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTg                        <  1:75626/50‑1 (MQ=255)
                                                                  gcATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGa  >  1:2884156/1‑71 (MQ=255)
                                                                   cATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTc                          >  1:518475/1‑46 (MQ=255)
                                                                   cATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTg   >  1:2216152/1‑69 (MQ=255)
                                                                    aTTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGa  >  1:2466544/1‑69 (MQ=255)
                                                                     ttttACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCg      <  1:2661559/64‑1 (MQ=255)
                                                                     ttttACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCg      <  1:2666302/64‑1 (MQ=255)
                                                                     |                                                                   
ACTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGA  >  minE/1484825‑1484961

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A