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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 821,760 G→A 50.0% intergenic (‑297/+157) ldrA ← / ← ldrC toxic polypeptide, small/toxic polypeptide, small

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE821,7600GA50.0% 32.2 / 142.4 104intergenic (‑297/+157)ldrA/ldrCtoxic polypeptide, small/toxic polypeptide, small
Reads supporting (aligned to +/- strand):  ref base G (22/30);  new base A (22/30);  total (44/60)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.18e-01

Only 100 of 107 total aligned reads displayed.

AATTCATCTTCACTTCATCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGAGAT  >  minE/821692‑821829
                                                                    |                                                                     
aaTTCATCTTCACTTCATCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTg                                                                       <  1:2788131/69‑1 (MQ=35)
     aTCTTCACTTCATCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGt                                                                <  1:3024025/71‑1 (MQ=39)
        ttcacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGtt                                                               >  1:3937129/1‑69 (MQ=40)
        ttcacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGt                                                                <  1:4887246/68‑1 (MQ=40)
        ttcacttcaTCCCTGAAATGTTTGCAATAAAGAGAACATTCCGGCTTTTCAACAGCTGTTGCAGTCGtt                                                               >  1:320400/1‑69 (MQ=255)
         tcacttcaTCCCTGAAATGTTTGCAATAAAGAGAACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTc                                                             <  1:576134/70‑1 (MQ=255)
          cacttcaTCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCa                                                            >  1:12353/1‑70 (MQ=11)
          cacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGttt                                                              <  1:1446410/68‑1 (MQ=40)
          cacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTc                                                             <  1:766275/69‑1 (MQ=40)
          cacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTc                                                             <  1:4797940/69‑1 (MQ=40)
          cacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTc                                                             <  1:2007512/69‑1 (MQ=40)
          cacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCa                                                            >  1:2046808/1‑70 (MQ=255)
          cacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCAt                                                           >  1:2184858/1‑71 (MQ=255)
           acttcaTCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCAt                                                           <  1:5603295/70‑1 (MQ=11)
           acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCAt                                                           <  1:2873495/70‑1 (MQ=255)
           acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCAt                                                           <  1:523176/70‑1 (MQ=255)
           acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCAt                                                           <  1:4844769/70‑1 (MQ=255)
           acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATg                                                          <  1:2383303/71‑1 (MQ=255)
           acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATg                                                          <  1:216736/71‑1 (MQ=255)
            cttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGa                                                         <  1:1444423/71‑1 (MQ=255)
               caTCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                         >  1:1055425/1‑68 (MQ=11)
                aTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGc                                                     <  1:1585178/71‑1 (MQ=255)
                 tCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCAt                                                           <  1:4156454/64‑1 (MQ=255)
                  cccTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGct                                                    >  1:5006544/1‑70 (MQ=255)
                    cTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTg                                                 <  1:4718052/71‑1 (MQ=17)
                      gAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGga                                               >  1:2975512/1‑71 (MQ=17)
                      gAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGctc                                                   >  1:3716784/1‑67 (MQ=255)
                       aaaTGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCAt                                                           <  1:1047272/58‑1 (MQ=11)
                       aaaTGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgat                                              <  1:2869499/71‑1 (MQ=17)
                       aaaTGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGgat                                              <  1:3996150/71‑1 (MQ=255)
                       aaaTGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGgat                                              <  1:3052047/71‑1 (MQ=255)
                       aaaTGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGgat                                              <  1:5206207/71‑1 (MQ=255)
                       aaaTGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGga                                               >  1:807401/1‑70 (MQ=255)
                        aaTGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgatg                                             <  1:3749695/71‑1 (MQ=18)
                            tttGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGc                                         >  1:385316/1‑71 (MQ=18)
                             ttGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgatg                                             >  1:4706826/1‑66 (MQ=18)
                             ttGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCt                                        >  1:1955198/1‑71 (MQ=18)
                             ttGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGc                                                                      >  1:2712986/1‑41 (MQ=38)
                              tGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgatgag                                           >  1:4322892/1‑66 (MQ=18)
                              tGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgatgag                                           >  1:5250076/1‑66 (MQ=18)
                              tGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCt                                        <  1:2690654/70‑1 (MQ=18)
                              tGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTg                                                      >  1:4844364/1‑56 (MQ=255)
                                 aaTGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTg                                                 <  1:1423380/58‑1 (MQ=17)
                                 aaTGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTg                                                 <  1:4827439/58‑1 (MQ=17)
                                  aTAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGc                                                                      <  1:4906049/36‑1 (MQ=40)
                                   tgaaGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATg                                                          <  1:4325493/45‑1 (MQ=14)
                                   tgaaGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATg                                                          <  1:1688084/45‑1 (MQ=14)
                                    aaaGAGTACATTCCGGCTTTTCAACAGCTGTTGCAg                                                                    >  1:2203093/1‑36 (MQ=33)
                                     aaGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgatga                                            >  1:504803/1‑59 (MQ=21)
                                     aaGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTc                                <  1:5614866/71‑1 (MQ=25)
                                       gagTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCgg                              >  1:3947259/1‑71 (MQ=37)
                                       gagTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCgg                              <  1:329877/71‑1 (MQ=37)
                                       gagTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCgg                              <  1:3616340/71‑1 (MQ=37)
                                       gagTGCATTCCGG‑TTTTTAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCggg                             >  1:1143634/1‑71 (MQ=255)
                                        agTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCa                                                            <  1:4530933/40‑1 (MQ=255)
                                        agTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGgatga                                            <  1:2635013/56‑1 (MQ=255)
                                         gtgcATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGt                            <  1:3826935/68‑1 (MQ=37)
                                          tgcATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgatga                                            >  1:2663971/3‑54 (MQ=25)
                                          tACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGt                                                       >  1:1192865/1‑43 (MQ=255)
                                          tACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGatgatg                                          >  1:4154224/1‑56 (MQ=255)
                                           aCATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTg                          >  1:4311177/1‑71 (MQ=255)
                                            cATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCAt                                                           >  1:5547527/1‑37 (MQ=17)
                                            cATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                         >  1:1312919/1‑39 (MQ=17)
                                             aTTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGcc                        <  1:501107/71‑1 (MQ=38)
                                              ttCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAg                                   <  1:1082392/59‑1 (MQ=37)
                                              ttCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAg                                   <  1:545143/59‑1 (MQ=37)
                                                ccGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                         >  1:650708/1‑35 (MQ=18)
                                                ccGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                         >  1:2092500/1‑35 (MQ=18)
                                                ccGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                         >  1:226352/1‑35 (MQ=18)
                                                ccGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCaa                      <  1:2800549/70‑1 (MQ=255)
                                                ccGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCaa                      <  1:5418685/70‑1 (MQ=255)
                                                 cGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGga                                               >  1:1791373/1‑44 (MQ=25)
                                                    tttttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                   <  1:21836/36‑1 (MQ=25)
                                                    tttttCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGt                            >  1:1653836/2‑60 (MQ=255)
                                                    tttttCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAat                     <  1:2084324/66‑1 (MQ=255)
                                                    cTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGc                                         >  1:2022357/1‑47 (MQ=255)
                                                    cTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGc                                         >  1:1070892/1‑47 (MQ=255)
                                                    cTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATAttt                 <  1:4230168/71‑1 (MQ=255)
                                                    cTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATAttt                 <  1:5015339/71‑1 (MQ=255)
                                                     ttttCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCtt                                       <  1:4371243/48‑1 (MQ=255)
                                                      tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                   <  1:1060769/35‑1 (MQ=25)
                                                      tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                   <  1:1971190/35‑1 (MQ=25)
                                                      tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                   <  1:1166742/35‑1 (MQ=25)
                                                      tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                   <  1:1424914/35‑1 (MQ=25)
                                                      tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                   <  1:1963204/35‑1 (MQ=25)
                                                      tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                   <  1:203470/35‑1 (MQ=25)
                                                      tttCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAata                    >  1:4012282/1‑66 (MQ=255)
                                                       ttCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTcc                                     >  1:1946119/1‑48 (MQ=255)
                                                       ttCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTcc                                     >  1:3830683/1‑48 (MQ=255)
                                                       ttCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTAc               <  1:412948/70‑1 (MQ=255)
                                                        tCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTcc                                     >  1:2781536/1‑47 (MQ=255)
                                                        tCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTcc                                     >  1:723886/1‑47 (MQ=255)
                                                        tCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCaa                      >  1:5660595/1‑62 (MQ=255)
                                                        tCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTa                <  1:3713959/68‑1 (MQ=255)
                                                        tCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTACCAGCTCGGGTTGCCa                       >  1:2337431/1‑61 (MQ=255)
                                                            cAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTgg         <  1:2585273/71‑1 (MQ=255)
                                                                tGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGaa       >  1:921513/1‑69 (MQ=255)
                                                                  ttGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCa                       <  1:5501011/51‑1 (MQ=255)
                                                                    gCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGAGAt  <  1:1084642/70‑1 (MQ=255)
                                                                    gCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGAGAt  <  1:3781259/70‑1 (MQ=255)
                                                                    |                                                                     
AATTCATCTTCACTTCATCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGAGAT  >  minE/821692‑821829

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