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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,919,234 G→A 21.6% F154F (TTC→TTT)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,2340GA21.6% 209.8 / 50.7 102F154F (TTC→TTT) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base G (33/47);  new base A (13/9);  total (46/56)
Fisher's exact test for biased strand distribution p-value = 1.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.56e-01

Only 100 of 108 total aligned reads displayed.

CCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCA  >  minE/2919164‑2919303
                                                                      |                                                                     
ccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                                                       <  1:1578336/71‑1 (MQ=255)
ccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                                                       <  1:478987/71‑1 (MQ=255)
    aGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACg                                                                   >  1:910126/1‑71 (MQ=255)
     gCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGc                                                                  >  1:2102341/1‑71 (MQ=255)
      cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                 <  1:1992691/71‑1 (MQ=255)
       ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                                                >  1:1117797/1‑71 (MQ=255)
       ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                                                >  1:1581253/1‑71 (MQ=255)
        tCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                                                       >  1:1166324/1‑63 (MQ=255)
        tCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                                                       >  1:2810286/1‑63 (MQ=255)
         ccaGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTg                                                              >  1:2974639/3‑71 (MQ=255)
         cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                               <  1:839445/70‑1 (MQ=255)
         cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                               <  1:299123/70‑1 (MQ=255)
         cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                 >  1:3835298/1‑68 (MQ=255)
         cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                 >  1:3850122/1‑68 (MQ=255)
          gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg                                                              <  1:3146009/70‑1 (MQ=255)
           aGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                                                            <  1:3287714/71‑1 (MQ=255)
             cATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGcccg                                                          >  1:3841291/1‑69 (MQ=255)
             cATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCgg                                                          <  1:886526/71‑1 (MQ=255)
             cATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCg                                                           <  1:694927/70‑1 (MQ=255)
              aTCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                                                            >  1:1172768/1‑68 (MQ=255)
               tCGAGTTGCCCATGTTGTTGCGCGCATAGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCctt                                                               >  1:1901390/1‑64 (MQ=255)
                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaa                                                      <  1:3745365/71‑1 (MQ=255)
                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaa                                                      <  1:2893689/71‑1 (MQ=255)
                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaa                                                      <  1:762208/71‑1 (MQ=255)
                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                       <  1:58346/70‑1 (MQ=255)
                 gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                       <  1:2583324/70‑1 (MQ=255)
                  aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                                                            <  1:1063702/64‑1 (MQ=255)
                  aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaaa                                                     <  1:3235175/71‑1 (MQ=255)
                  aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaaa                                                     >  1:3741343/1‑71 (MQ=255)
                   gttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTaaa                                                                     >  1:82953/2‑54 (MQ=255)
                   aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc                                                                    <  1:3546383/55‑1 (MQ=255)
                   aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc                                                                    <  1:2687687/55‑1 (MQ=255)
                   aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc                                                                    <  1:668902/55‑1 (MQ=255)
                     tGCCCATGTTGTTGCACGCATCGCCCGCGTAGACCAGCGTCATATCGTTAAACGc                                                                  >  1:1316265/1‑55 (MQ=255)
                      gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                               >  1:2686168/1‑57 (MQ=255)
                      gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCt                                                 >  1:554028/1‑71 (MQ=255)
                       cccATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGc                                                        <  1:3755735/63‑1 (MQ=255)
                        ccATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTcc                                               <  1:3782032/71‑1 (MQ=255)
                         cATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCt                                              >  1:3347436/1‑71 (MQ=255)
                          aTGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTg                                             <  1:1265581/71‑1 (MQ=255)
                          aTGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGc                                                  <  1:2935722/66‑1 (MQ=255)
                           tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                                                >  1:2627365/1‑67 (MQ=255)
                           tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                                             >  1:2860423/1‑70 (MQ=255)
                           tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                                             >  1:793078/1‑70 (MQ=255)
                             ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa                                           <  1:2089736/70‑1 (MQ=255)
                             ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa                                           <  1:1330796/70‑1 (MQ=255)
                             ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa                                           <  1:789498/70‑1 (MQ=255)
                             ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCAt                                          >  1:1159080/1‑71 (MQ=255)
                             ttgttACGCGCGTCACCTGCATAGACAAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGAAt                                          >  1:1735195/1‑71 (MQ=255)
                              tgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATg                                         >  1:2304940/1‑71 (MQ=255)
                              tgttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCAt                                          <  1:465540/70‑1 (MQ=255)
                               gttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATgg                                        >  1:2865924/1‑71 (MQ=255)
                               gttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATg                                         <  1:2745274/70‑1 (MQ=255)
                                ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATgg                                        <  1:358280/70‑1 (MQ=255)
                                ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATgg                                        <  1:1224030/70‑1 (MQ=255)
                                  gcgcgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCa                                                       >  1:3906515/2‑53 (MQ=255)
                                  gcgcgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCa                                                       >  1:428561/2‑53 (MQ=255)
                                  aCGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGt                                       >  1:291980/1‑69 (MQ=255)
                                  aCGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTg                                      <  1:3118263/70‑1 (MQ=255)
                                   cgcgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGtca                                     <  1:414890/70‑3 (MQ=255)
                                    gcgcgTCACCTGCATAGACAAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTgag                                    >  1:3389424/1‑70 (MQ=255)
                                      gcgTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                       <  1:124757/49‑1 (MQ=255)
                                           aCCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                                                >  1:331443/1‑35 (MQ=255)
                                           aCCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                                                >  1:3142143/1‑35 (MQ=255)
                                             cTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGagaaga                                <  1:1332913/65‑1 (MQ=255)
                                               gCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATgg                                        <  1:1371044/55‑1 (MQ=255)
                                               gCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                        >  1:2729199/1‑71 (MQ=255)
                                               gCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                        >  1:1443836/1‑71 (MQ=255)
                                                cATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                        <  1:2524156/70‑1 (MQ=255)
                                                cATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                        >  1:215778/1‑70 (MQ=255)
                                                  tAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcagcag                     >  1:1566546/1‑71 (MQ=255)
                                                   aGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCagcagc                    >  1:345191/1‑71 (MQ=255)
                                                    gACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCt                   <  1:1845784/71‑1 (MQ=255)
                                                    gACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCt                   <  1:488704/71‑1 (MQ=255)
                                                    gACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCt                   <  1:678766/71‑1 (MQ=255)
                                                    gACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCt                   >  1:2324041/1‑71 (MQ=255)
                                                     aCCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCcagca                      <  1:1536491/67‑1 (MQ=255)
                                                      ccAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGc                 <  1:417966/71‑1 (MQ=255)
                                                       cAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGagaa                                  >  1:3417191/1‑53 (MQ=255)
                                                       cAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCg                >  1:898756/1‑71 (MQ=255)
                                                            tcctttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGa           <  1:1672665/68‑1 (MQ=255)
                                                            tCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGa           <  1:1495109/71‑1 (MQ=255)
                                                             cATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGAt          >  1:3709877/1‑71 (MQ=255)
                                                              atctCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTCGGGTg         <  1:2544862/68‑1 (MQ=255)
                                                              aTTTCGTTGAACGCTTTGCCTGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATg         <  1:1517941/71‑1 (MQ=255)
                                                               tttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATg                                         <  1:3224539/38‑1 (MQ=255)
                                                               tttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGTGAAGATCCGCCAGCAGCTGCGTGGGATgg        <  1:2800/71‑1 (MQ=255)
                                                               tttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg        <  1:1516533/71‑1 (MQ=255)
                                                               tttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg        <  1:291035/71‑1 (MQ=255)
                                                               tttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGAATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg        <  1:2940543/71‑1 (MQ=255)
                                                                ttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCa                                           >  1:2885270/1‑35 (MQ=255)
                                                                  cGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAAc     >  1:464517/1‑71 (MQ=255)
                                                                  cGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAAc     >  1:3500525/1‑71 (MQ=255)
                                                                   gTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTCGGGTGGaa      <  1:3462692/69‑1 (MQ=255)
                                                                    ttGAACGCTTTGCCGGGCAAATGGTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg        >  1:16463/1‑66 (MQ=255)
                                                                    ttGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTc   <  1:1671315/71‑1 (MQ=255)
                                                                    ttGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTc   <  1:1014133/71‑1 (MQ=255)
                                                                     tGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGTATGGAACTCa  >  1:242989/1‑71 (MQ=255)
                                                                     tGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTc   <  1:856089/70‑1 (MQ=255)
                                                                      gAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATTGAACTCa  <  1:2928175/70‑1 (MQ=255)
                                                                      |                                                                     
CCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCA  >  minE/2919164‑2919303

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