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
A5 F1 I0 R2 201 99.6 7939938 96.9% 7693799 60.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,280 T→C 100% pseudogene (413/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,2800TC99.1% 387.2 / ‑4.6 115pseudogene (413/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (42/70);  total (43/72)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 115 total aligned reads displayed.

CTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCC  >  W3110S.gb/3824212‑3824347
                                                                    |                                                                   
cTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAg                                                                   <  1:2903170/71‑1 (MQ=255)
    gACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc                                                               <  1:379739/71‑1 (MQ=255)
      cGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgcgc                                                             <  1:2497189/71‑1 (MQ=255)
        tGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTa                                                           >  1:4387775/1‑71 (MQ=255)
          cTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAg                                                                   <  1:2307475/61‑1 (MQ=255)
          cTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTAc                                                          <  1:525704/70‑1 (MQ=255)
          cTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACa                                                         <  1:5258771/71‑1 (MQ=255)
          cTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGG‑‑GATGCGCTACAGa                                                       <  1:5517403/71‑1 (MQ=255)
            tCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGAt                                                                 >  1:5764852/1‑61 (MQ=255)
             cAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAg                                                        >  1:7676913/1‑69 (MQ=255)
             cAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAg                                                        >  1:461480/1‑69 (MQ=255)
             cAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa                                                       <  1:1314457/70‑1 (MQ=255)
             cAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa                                                       <  1:1685815/70‑1 (MQ=255)
                 cTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtg                                                  <  1:6170368/71‑1 (MQ=255)
                    aTGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCtgg                                                 <  1:627971/69‑1 (MQ=255)
                    aTGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtgg                                                 <  1:1520830/69‑1 (MQ=255)
                     tggtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtggtgg                                              <  1:5371854/71‑1 (MQ=255)
                     tggtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtggtgg                                              <  1:7194056/71‑1 (MQ=255)
                      ggtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtggtgg                                              >  1:5500477/1‑70 (MQ=255)
                      ggtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCCGGCAGATGCGCTACAGAAGCtggtgg                                              >  1:1140173/1‑70 (MQ=255)
                          gCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGaaaa                                          <  1:1937486/70‑1 (MQ=255)
                          gCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGaaaa                                          <  1:5922027/70‑1 (MQ=255)
                          gCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGaaaa                                          <  1:1700001/70‑1 (MQ=255)
                          gCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAAc                                         <  1:7302957/71‑1 (MQ=255)
                          gCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAAc                                         <  1:5782816/71‑1 (MQ=255)
                          gCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAAc                                         <  1:7884568/71‑1 (MQ=255)
                            aCGCGTACCGCGTCGATTACTGGTGCCTTCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGTAAAACgg                                       <  1:2425054/71‑1 (MQ=255)
                            aCGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACgg                                       <  1:1549629/71‑1 (MQ=255)
                             cgcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACgg                                       >  1:7748245/1‑70 (MQ=255)
                             cgcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGc                                      <  1:6223392/71‑1 (MQ=255)
                             cgcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGc                                      <  1:7378073/71‑1 (MQ=255)
                             cgcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGc                                      <  1:7274332/71‑1 (MQ=255)
                              gcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGc                                      >  1:3687253/1‑70 (MQ=255)
                                gTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGAt                                                                 >  1:4415370/1‑41 (MQ=255)
                                gTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg                                   <  1:5505038/71‑1 (MQ=255)
                                gTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAg                                   >  1:6432314/1‑71 (MQ=255)
                                 tACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtg                                                  <  1:179363/55‑1 (MQ=255)
                                 tACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTTGaaa                                           <  1:4099679/62‑1 (MQ=255)
                                  aCCGCGTCGATTACGGGTTCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCt                                 >  1:4168679/1‑71 (MQ=255)
                                  aCCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCt                                 >  1:5293152/1‑71 (MQ=255)
                                   ccGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTg                                <  1:1292001/71‑1 (MQ=255)
                                    cgcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGa                               <  1:2198717/71‑1 (MQ=255)
                                     gcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGa                               >  1:7325733/1‑70 (MQ=255)
                                     gcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGa                               >  1:2848510/1‑70 (MQ=255)
                                      cgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaaa                             <  1:3122085/71‑1 (MQ=255)
                                        tCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTg                                <  1:4919026/66‑1 (MQ=255)
                                        tCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAc                           >  1:6181729/1‑71 (MQ=255)
                                        tCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAc                           >  1:1924178/1‑71 (MQ=255)
                                          gATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc                          <  1:5274160/70‑1 (MQ=255)
                                          gATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc                          <  1:7031862/70‑1 (MQ=255)
                                           aTTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtgg                                                 <  1:6534664/46‑1 (MQ=255)
                                           aTTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtgg                                                 <  1:2436273/46‑1 (MQ=255)
                                               cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc                     <  1:1177173/70‑1 (MQ=255)
                                                 ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                  <  1:5557385/71‑1 (MQ=255)
                                                  gTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                  >  1:4590189/1‑70 (MQ=255)
                                                   tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtg                                                  <  1:6203644/37‑1 (MQ=255)
                                                   tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg                 >  1:1080058/1‑70 (MQ=255)
                                                     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCaa                        <  1:5001909/61‑1 (MQ=255)
                                                     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCaa                        <  1:4527163/61‑1 (MQ=255)
                                                     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCaa                        <  1:4909611/61‑1 (MQ=255)
                                                     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa               <  1:2116255/70‑1 (MQ=255)
                                                     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa               <  1:4128279/70‑1 (MQ=255)
                                                     ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTCGTGGAAAACGGCAAGCTGAAAACCaa                        <  1:2085199/61‑1 (MQ=255)
                                                      cTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaaa                             >  1:718242/1‑55 (MQ=255)
                                                      cTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaaa                             >  1:210471/1‑55 (MQ=255)
                                                       tGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCaa                                    <  1:2644283/47‑1 (MQ=255)
                                                       tGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCaa                                    <  1:6448284/47‑1 (MQ=255)
                                                        gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaaaa                            >  1:4761077/1‑54 (MQ=255)
                                                        gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaaaa                            >  1:4016814/1‑54 (MQ=255)
                                                        gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaaaa                            >  1:2154752/1‑54 (MQ=255)
                                                        gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg            >  1:3490256/1‑70 (MQ=255)
                                                        gCGTGGCGCTGGAAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg            >  1:3934252/1‑70 (MQ=255)
                                                         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaaa                             >  1:1179421/1‑52 (MQ=255)
                                                         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg            <  1:6426984/69‑1 (MQ=255)
                                                         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg            <  1:4165145/69‑1 (MQ=255)
                                                         cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa          >  1:5239686/1‑71 (MQ=255)
                                                          gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCg                    >  1:7556082/1‑60 (MQ=255)
                                                          gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg            <  1:6789656/68‑1 (MQ=255)
                                                          gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg            <  1:2682429/68‑1 (MQ=255)
                                                          gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt         <  1:1309421/71‑1 (MQ=255)
                                                           tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg            >  1:4012229/1‑67 (MQ=255)
                                                           tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt         <  1:3033789/70‑1 (MQ=255)
                                                           tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg        <  1:4544927/71‑1 (MQ=255)
                                                           tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg        <  1:6316859/71‑1 (MQ=255)
                                                           tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg        >  1:2794168/1‑71 (MQ=255)
                                                            ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa              <  1:2887925/64‑1 (MQ=255)
                                                            ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg       >  1:989217/1‑71 (MQ=255)
                                                            ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg       >  1:2794583/1‑71 (MQ=255)
                                                            ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg       >  1:7541537/1‑71 (MQ=255)
                                                             gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt      <  1:5896493/71‑1 (MQ=255)
                                                              cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa              <  1:4865215/62‑1 (MQ=255)
                                                              cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa              <  1:2149409/62‑1 (MQ=255)
                                                               gcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa     <  1:3462428/70‑1 (MQ=255)
                                                               gcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa     <  1:5320133/70‑1 (MQ=255)
                                                                cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCa                         <  1:4588381/49‑1 (MQ=255)
                                                                 tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc                          <  1:4688594/47‑1 (MQ=255)
                                                                 tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg        >  1:3154710/1‑65 (MQ=255)
                                                                 tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc  >  1:2854874/1‑71 (MQ=255)
                                                                 tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc  >  1:2408628/1‑71 (MQ=255)
                                                                 tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc  >  1:5718457/1‑71 (MQ=255)
                                                                    |                                                                   
CTGCGACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCC  >  W3110S.gb/3824212‑3824347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A