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 821,766 G→A 50.5% intergenic (‑303/+151) ldrA ← / ← ldrC toxic polypeptide, small/toxic polypeptide, small

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE821,7660GA50.5% 29.3 / 149.4 107intergenic (‑303/+151)ldrA/ldrCtoxic polypeptide, small/toxic polypeptide, small
Reads supporting (aligned to +/- strand):  ref base G (20/33);  new base A (23/31);  total (43/64)
Fisher's exact test for biased strand distribution p-value = 6.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 110 total aligned reads displayed.

ATCTTCACTTCATCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGAGATA  >  minE/821697‑821830
                                                                     |                                                                
aTCTTCACTTCATCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGt                                                                 <  1:3024025/71‑1 (MQ=39)
   ttcacttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGt                                                                 <  1:4887246/68‑1 (MQ=40)
    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                                                            <  1:523176/70‑1 (MQ=255)
      acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCAt                                                            <  1:2873495/70‑1 (MQ=255)
      acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCAt                                                            <  1:4844769/70‑1 (MQ=255)
      acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATg                                                           <  1:216736/71‑1 (MQ=255)
      acttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATg                                                           <  1:2383303/71‑1 (MQ=255)
       cttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTc                                                              <  1:5234717/67‑1 (MQ=40)
       cttcaTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGa                                                          <  1:1444423/71‑1 (MQ=255)
          caTCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                          >  1:1055425/1‑68 (MQ=11)
          caTCCCTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTg                                                       >  1:3842299/1‑71 (MQ=14)
           aTCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGc                                                      <  1:1585178/71‑1 (MQ=255)
            tCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCAt                                                            <  1:4156454/64‑1 (MQ=255)
               cTGAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTg                                                  <  1:4718052/71‑1 (MQ=17)
                 gAAATGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGga                                                >  1:2975512/1‑71 (MQ=17)
                 gAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGctc                                                    >  1:3716784/1‑67 (MQ=255)
                 gAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGctc                                                    >  1:2800009/1‑67 (MQ=255)
                  aaaTGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCAt                                                            <  1:1047272/58‑1 (MQ=11)
                  aaaTGTTTGCAATGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgat                                               <  1:2869499/71‑1 (MQ=17)
                  aaaTGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTgg                                                 <  1:4647999/69‑1 (MQ=255)
                  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)
                         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                                                  <  1:4827439/58‑1 (MQ=17)
                            aaTGAAGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTg                                                  <  1:1423380/58‑1 (MQ=17)
                              tgaaGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATg                                                           <  1:4325493/45‑1 (MQ=14)
                              tgaaGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATg                                                           <  1:1688084/45‑1 (MQ=14)
                                aaGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGgatga                                             >  1:504803/1‑59 (MQ=21)
                                aaGAGTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTc                                 <  1:5614866/71‑1 (MQ=25)
                                  gagTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCgg                               <  1:3616340/71‑1 (MQ=37)
                                  gagTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCgg                               >  1:3947259/1‑71 (MQ=37)
                                  gagTGCATTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCgg                               <  1:329877/71‑1 (MQ=37)
                                  gagTGCATTCCGG‑TTTTTAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCggg                              >  1:1143634/1‑71 (MQ=255)
                                   agTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCa                                                             <  1:4530933/40‑1 (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)
                                        aTTCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGcc                         <  1:501107/71‑1 (MQ=38)
                                         ttCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAg                                    <  1:545143/59‑1 (MQ=37)
                                         ttCCGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAg                                    <  1:1082392/59‑1 (MQ=37)
                                           ccGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                          >  1:2092500/1‑35 (MQ=18)
                                           ccGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                          >  1:226352/1‑35 (MQ=18)
                                           ccGGTTTTTCAACAGCTGTTACAGTCATTTCATGa                                                          >  1:650708/1‑35 (MQ=18)
                                           ccGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCaa                       <  1:2800549/70‑1 (MQ=255)
                                           ccGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCaa                       <  1:5418685/70‑1 (MQ=255)
                                            cGGTTTTTCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGga                                                >  1:1791373/1‑44 (MQ=25)
                                            cGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCgg                               <  1:2158097/61‑1 (MQ=255)
                                               tttttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                    <  1:21836/36‑1 (MQ=25)
                                               tttttCAACAGCTGTTACAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGt                             >  1:1653836/2‑60 (MQ=255)
                                               cTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGc                                          >  1:2022357/1‑47 (MQ=255)
                                               cTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGc                                          >  1:1070892/1‑47 (MQ=255)
                                               cTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATAttt                  <  1:5015339/71‑1 (MQ=255)
                                               cTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATAttt                  <  1:4230168/71‑1 (MQ=255)
                                                 tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                    <  1:1424914/35‑1 (MQ=25)
                                                 tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                    <  1:1060769/35‑1 (MQ=25)
                                                 tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                    <  1:1483111/35‑1 (MQ=25)
                                                 tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                    <  1:1166742/35‑1 (MQ=25)
                                                 tttCAACAGCTGTTACAGTCATTTCATGAGTGctc                                                    <  1:1971190/35‑1 (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                                      >  1:723886/1‑47 (MQ=255)
                                                   tCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTcc                                      >  1:2781536/1‑47 (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)
                                                               acAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGaa        >  1:1986682/2‑65 (MQ=255)
                                                                cAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGAGATa  <  1:2591327/70‑1 (MQ=255)
                                                                cAGTCATTTCATGAGTGCTCTGGATGAGGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGTGATa  <  1:5597983/70‑1 (MQ=255)
                                                                   tCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTa                 <  1:1360273/52‑1 (MQ=255)
                                                                     gTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTAc                >  1:4856740/1‑51 (MQ=255)
                                                                     gTTTCATGAGTGCTCTGGATGATGCTTCCAGCTAGGGTTGCCAATATTTAc                >  1:1330868/1‑51 (MQ=255)
                                                                     |                                                                
ATCTTCACTTCATCCCTGAAATGTTTGCAATAAAGAGTACATTCCGGCTTTTCAACAGCTGTTGCAGTCGTTTCATGAGTGCTCTGGATGATGCTTCCAGCTCGGGTTGCCAATATTTACTTGTGGAAGAGATA  >  minE/821697‑821830

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