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 2,919,228 T→C 20.8% E156E (GAA→GAG)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,2280TC20.8% 202.4 / 50.1 102E156E (GAA→GAG) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base T (34/46);  new base C (13/8);  total (48/54)
Fisher's exact test for biased strand distribution p-value = 1.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

Only 100 of 113 total aligned reads displayed.

AAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGG  >  minE/2919159‑2919297
                                                                     |                                                                     
aaGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAttt                                                                      >  1:721565/1‑71 (MQ=255)
aaGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAtt                                                                       >  1:3856891/1‑70 (MQ=255)
 aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                                                     <  1:910884/71‑1 (MQ=255)
 aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                                                     >  1:740140/1‑71 (MQ=255)
 aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGAATAGACCAGCGTCATTTc                                                                     >  1:2800822/1‑71 (MQ=255)
   cgccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGGCACCTGCATAGACCAGCGTCATTTCGt                                                                   <  1:1808402/71‑1 (MQ=255)
    gccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGtt                                                                  <  1:199087/71‑1 (MQ=255)
     ccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                                                 <  1:1578336/71‑1 (MQ=255)
     ccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                                                 <  1:478987/71‑1 (MQ=255)
       gcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGttaac                                                               >  1:3249707/1‑68 (MQ=255)
         aGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACg                                                             >  1:910126/1‑71 (MQ=255)
          gCTTCCAGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGc                                                            >  1:2102341/1‑71 (MQ=255)
           cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                           <  1:1992691/71‑1 (MQ=255)
           cTTCGAGCAGCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGt                                                                   <  1:365812/63‑1 (MQ=255)
           cTTCGAGCAGCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGt                                                                   <  1:361106/63‑1 (MQ=255)
            ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                                          >  1:1581253/1‑71 (MQ=255)
            ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCtt                                                          >  1:1117797/1‑71 (MQ=255)
             tCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                                                 >  1:2810286/1‑63 (MQ=255)
             tCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg                                                                 >  1:1166324/1‑63 (MQ=255)
              ccaGCATCGAGTTGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTg                                                        >  1:2974639/3‑71 (MQ=255)
              cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                         <  1:299123/70‑1 (MQ=255)
              cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                           >  1:3835298/1‑68 (MQ=255)
              cGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCt                                                           >  1:3850122/1‑68 (MQ=255)
               gAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTg                                                        <  1:1436368/70‑1 (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                                                 <  1:58346/70‑1 (MQ=255)
                      gAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                 <  1:2583324/70‑1 (MQ=255)
                       aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc                                                      <  1:1063702/64‑1 (MQ=255)
                       aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaaa                                               >  1:3741343/1‑71 (MQ=255)
                       aaTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCaaa                                               <  1:3235175/71‑1 (MQ=255)
                        gttGCCCATGTTGTTGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTaaa                                                               >  1:82953/2‑54 (MQ=255)
                        aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAtt                                                                       <  1:890348/46‑1 (MQ=255)
                        aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc                                                              <  1:2687687/55‑1 (MQ=255)
                        aTTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc                                                              <  1:3546383/55‑1 (MQ=255)
                           gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCttt                                                         >  1:2686168/1‑57 (MQ=255)
                           gCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCt                                           >  1:554028/1‑71 (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)
                                tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                                                                     <  1:243703/40‑1 (MQ=255)
                                tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTc                                          >  1:2627365/1‑67 (MQ=255)
                                tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                                       >  1:793078/1‑70 (MQ=255)
                                tgttgtTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTg                                       >  1:2860423/1‑70 (MQ=255)
                                 gttgttGCGCGCATCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCa                                     >  1:2923270/1‑71 (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)
                                     ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATgg                                  <  1:358280/70‑1 (MQ=255)
                                     ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATgg                                  <  1:1224030/70‑1 (MQ=255)
                                     ttACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGt                                 <  1:1745529/71‑1 (MQ=255)
                                       gcgcgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCa                                                 >  1:428561/2‑53 (MQ=255)
                                       gcgcgcaTCGCCCGCGTAGACCAGCGTCATCTCGTTAAACGCCTTGCCCGGCa                                                 >  1:3906515/2‑53 (MQ=255)
                                       aCGCGCGTCACCTGCATAGACCAGCGTCATTTCGtt                                                                  >  1:861328/1‑36 (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)
                                           gcgTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCa                                                 <  1:2678815/49‑1 (MQ=255)
                                              tCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATc                        <  1:984147/71‑1 (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)
                                                    gCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                  >  1:3375487/1‑71 (MQ=255)
                                                     cATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                  <  1:2524156/70‑1 (MQ=255)
                                                     cATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcag                  >  1:215778/1‑70 (MQ=255)
                                                       tAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCcagcag               >  1:1566546/1‑71 (MQ=255)
                                                       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)
                                                          aCCAGCGTCATCTCGTTAAACGCCTTGCCCGGCAGGTGCTCCTGCATGGTCATCAGGTCCGCcagca                <  1:1536491/67‑1 (MQ=255)
                                                           ccAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGc           <  1:417966/71‑1 (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)
                                                                   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)
                                                                     |                                                                     
AAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCCGGGCAAATGCTCCTGCATGGTGAGAAGATCCGCCAGCAGCTGCGTGGGATGG  >  minE/2919159‑2919297

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