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 2,919,240 T→C 23.1% K152K (AAA→AAG)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,2400TC23.1% 172.0 / 53.3 95K152K (AAA→AAG) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base T (26/47);  new base C (11/11);  total (37/58)
Fisher's exact test for biased strand distribution p-value = 3.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

Only 100 of 107 total aligned reads displayed.

CTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGT  >  minE/2919170‑2919308
                                                                      |                                                                    
cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                      <  1:1992691/71‑1 (MQ=255)
 ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                                                     >  1:1117797/1‑71 (MQ=255)
 ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                                                     >  1:1581253/1‑71 (MQ=255)
   ccaGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTg                                                                   >  1:2974639/3‑71 (MQ=255)
   cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                                    <  1:299123/70‑1 (MQ=255)
   cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                                    <  1:839445/70‑1 (MQ=255)
   cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                      >  1:3850122/1‑68 (MQ=255)
   cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                                      >  1:3835298/1‑68 (MQ=255)
    gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg                                                                   <  1:3146009/70‑1 (MQ=255)
    gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg                                                                   <  1:1436368/70‑1 (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                                                           <  1:2893689/71‑1 (MQ=255)
           gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaa                                                           <  1:3745365/71‑1 (MQ=255)
           gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaa                                                           <  1:762208/71‑1 (MQ=255)
           gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                            <  1:2583324/70‑1 (MQ=255)
           gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                            <  1:58346/70‑1 (MQ=255)
            aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                                                                 <  1:1063702/64‑1 (MQ=255)
            aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaaa                                                          <  1:3235175/71‑1 (MQ=255)
                gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                                    >  1:2686168/1‑57 (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)
                      gttgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa                                                >  1:2923270/1‑71 (MQ=255)
                       ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa                                                <  1:789498/70‑1 (MQ=255)
                       ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa                                                <  1:2089736/70‑1 (MQ=255)
                       ttgttgCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa                                                <  1:1330796/70‑1 (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)
                          ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGt                                            <  1:1745529/71‑1 (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                                                            <  1:2678815/49‑1 (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                             >  1:1443836/1‑71 (MQ=255)
                                         gCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                             >  1:3375487/1‑71 (MQ=255)
                                         gCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                             >  1:2729199/1‑71 (MQ=255)
                                          cATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                             <  1:2524156/70‑1 (MQ=255)
                                            tAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcagcag                          >  1:1566546/1‑71 (MQ=255)
                                            tAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcagcag                          >  1:3820175/1‑71 (MQ=255)
                                             aGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCagcagc                         >  1:345191/1‑71 (MQ=255)
                                              gACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCt                        <  1:488704/71‑1 (MQ=255)
                                              gACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCt                        <  1:678766/71‑1 (MQ=255)
                                              gACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCt                        <  1:1845784/71‑1 (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)
                                                         tttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg             <  1:291035/71‑1 (MQ=255)
                                                         tttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGAATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg             <  1:2940543/71‑1 (MQ=255)
                                                          ttCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCa                                                >  1:2885270/1‑35 (MQ=255)
                                                            cGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAAc          >  1:3500525/1‑71 (MQ=255)
                                                            cGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAAc          >  1:464517/1‑71 (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)
                                                               tGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCa       >  1:632586/1‑71 (MQ=255)
                                                                gAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATTGAACTCa       <  1:2928175/70‑1 (MQ=255)
                                                                 aaCGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATgg             <  1:3392923/63‑1 (MQ=255)
                                                                 aaCGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCAt      <  1:935183/70‑1 (MQ=255)
                                                                 aaCGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTCGGGTGGAACTcgt      <  1:3478967/70‑3 (MQ=255)
                                                                 aaCGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTGGGTCGGGTGGAACTcgt      <  1:1989517/70‑3 (MQ=255)
                                                                  aCGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCCAGCAGCTgg                      >  1:705940/1‑52 (MQ=255)
                                                                   cGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGAt                                    >  1:1315962/1‑38 (MQ=255)
                                                                    gCTTTGCCGGGCAATTGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGt  <  1:2727425/71‑1 (MQ=255)
                                                                    gCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGt  <  1:56103/71‑1 (MQ=255)
                                                                    gCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGt  <  1:2405156/71‑1 (MQ=255)
                                                                      tttGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGt  >  1:25113/1‑69 (MQ=255)
                                                                      |                                                                    
CTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGGAACTCATTGGT  >  minE/2919170‑2919308

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