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 834,635 C→T 20.0% H1031H (CAC→CAT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE834,6350CT20.0% 258.3 / 53.8 125H1031H (CAC→CAT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (50/50);  new base T (15/10);  total (65/60)
Fisher's exact test for biased strand distribution p-value = 5.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.16e-01

Only 100 of 128 total aligned reads displayed.

TCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTG  >  minE/834565‑834702
                                                                      |                                                                   
tctcCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCAc                                                                     >  1:422689/1‑71 (MQ=255)
tctcCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCAc                                                                     >  1:3109015/1‑71 (MQ=255)
    cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAga                                                                 <  1:3325402/71‑2 (MQ=255)
    cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGc                                                                 >  1:2279472/1‑71 (MQ=255)
    cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGc                                                                 >  1:3771642/1‑71 (MQ=255)
    cAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAgt                                                                 >  1:3245122/1‑70 (MQ=255)
         cGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGa                                                                   >  1:5564691/1‑64 (MQ=255)
           aCCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATcc                                                           >  1:3053275/1‑70 (MQ=255)
            ccTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         <  1:2859978/71‑1 (MQ=255)
              tggtctggtcTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATg                                                       >  1:4345503/1‑71 (MQ=255)
                gtctggtctgGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGc                                                     >  1:1666562/1‑71 (MQ=255)
                gtccggtctgGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTgg                                                      <  1:4443603/70‑1 (MQ=255)
                  ccggtctggAAAGAGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGc                                                     >  1:2991480/3‑69 (MQ=255)
                   tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         <  1:1256267/64‑1 (MQ=255)
                   tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         <  1:1249383/64‑1 (MQ=255)
                   tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         <  1:1082990/64‑1 (MQ=255)
                     gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGt                                                   <  1:191628/68‑1 (MQ=255)
                     gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTAc                                                 <  1:4367756/70‑1 (MQ=255)
                     gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTAc                                                 <  1:3967120/70‑1 (MQ=255)
                     gtctggAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACg                                                >  1:4241321/1‑71 (MQ=255)
                      tctggATGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTg                                                               <  1:3257601/55‑1 (MQ=255)
                       ctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGct                                              >  1:2064287/1‑71 (MQ=255)
                        tggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGc                                               <  1:4808438/69‑1 (MQ=255)
                          gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc                                           <  1:1764458/71‑1 (MQ=255)
                          gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc                                           <  1:1157887/71‑1 (MQ=255)
                          gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc                                           >  1:5173350/1‑71 (MQ=255)
                            aGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                                         <  1:1013436/71‑1 (MQ=255)
                             gATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATcc                                                           <  1:5523829/52‑1 (MQ=255)
                               tGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctcac                                           >  1:223304/1‑64 (MQ=255)
                                gAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATcc                                                           <  1:4209999/49‑1 (MQ=255)
                                gAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcg                                     >  1:1469327/1‑71 (MQ=255)
                                 aaCACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                    <  1:2843237/71‑1 (MQ=255)
                                  acacGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         <  1:2550197/49‑1 (MQ=255)
                                  acacGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         <  1:2962516/49‑1 (MQ=255)
                                    acGTTTCTTACAACGCCGGTTACACCAACGTTCACGAg                                                                  >  1:4555694/1‑38 (MQ=255)
                                    acGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAg                                 >  1:5009384/1‑71 (MQ=255)
                                    acGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAg                                 <  1:266260/71‑1 (MQ=255)
                                     cGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAg                                 >  1:1435995/1‑70 (MQ=255)
                                       tttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATgg                                                      <  1:3958168/47‑1 (MQ=255)
                                       tttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCaa                              >  1:538620/1‑71 (MQ=255)
                                        ttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATc                                                            >  1:1707135/1‑40 (MQ=255)
                                        ttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc                                >  1:814090/1‑68 (MQ=255)
                                        ttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc                                >  1:4392780/1‑68 (MQ=255)
                                        ttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc                                >  1:2614700/1‑68 (MQ=255)
                                         tCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         >  1:3060372/1‑42 (MQ=255)
                                         tCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         >  1:174100/1‑42 (MQ=255)
                                         tCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACt                            >  1:1481969/1‑71 (MQ=255)
                                          cTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgt                                       >  1:2537173/1‑59 (MQ=255)
                                          cTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgt                                       >  1:3420004/1‑59 (MQ=255)
                                           ttACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                                         >  1:1369880/1‑56 (MQ=255)
                                           ttACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                                         >  1:863518/1‑56 (MQ=255)
                                            tACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                                         <  1:1398375/39‑1 (MQ=255)
                                             ataaCGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTAt                        >  1:924770/3‑71 (MQ=255)
                                              taaCGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATc                       <  1:4506961/70‑1 (MQ=255)
                                              cAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGc                                                     >  1:1838750/1‑41 (MQ=255)
                                              cAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGc                                                     >  1:2665952/1‑41 (MQ=255)
                                              cAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATc                       <  1:3411846/71‑1 (MQ=255)
                                               aaCGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTAt                        >  1:3529316/1‑69 (MQ=255)
                                               aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTAt                        >  1:2246712/1‑69 (MQ=255)
                                               aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                      <  1:5049300/71‑1 (MQ=255)
                                               aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                      <  1:3459054/71‑1 (MQ=255)
                                               aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                      <  1:615685/71‑1 (MQ=255)
                                               aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                      <  1:1352667/71‑1 (MQ=255)
                                                aCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctc                                             <  1:5262474/47‑1 (MQ=255)
                                                aCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctc                                             <  1:4091012/47‑1 (MQ=255)
                                                  gCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGa                   <  1:4554497/71‑1 (MQ=255)
                                                    cGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                 <  1:1855271/71‑1 (MQ=255)
                                                       ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc              <  1:3237351/71‑1 (MQ=255)
                                                       ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc              <  1:1293817/71‑1 (MQ=255)
                                                       atACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCatc              >  1:3748264/2‑69 (MQ=255)
                                                        tACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGa                   <  1:4099391/65‑1 (MQ=255)
                                                        tACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCatcc             >  1:1238355/1‑68 (MQ=255)
                                                        tACACCAACGTTCACGAGCTGATCCCATGGCGTACGctc                                             >  1:4909502/1‑39 (MQ=255)
                                                        tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc               >  1:906431/1‑69 (MQ=255)
                                                        tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc               >  1:3780668/1‑69 (MQ=255)
                                                        tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc               >  1:2056047/1‑69 (MQ=255)
                                                         acacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg            >  1:3413186/1‑71 (MQ=255)
                                                         acacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg            >  1:1594438/1‑71 (MQ=255)
                                                         acacAAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg            >  1:2207608/1‑71 (MQ=255)
                                                           acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAg                     <  1:3148503/60‑1 (MQ=255)
                                                           acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg          <  1:1309397/71‑1 (MQ=255)
                                                           acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg          >  1:5194684/1‑71 (MQ=255)
                                                           acCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                    <  1:2697382/45‑1 (MQ=255)
                                                            ccAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg          <  1:3916310/70‑1 (MQ=255)
                                                             cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTgg         >  1:4225396/1‑70 (MQ=255)
                                                             cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTgg         >  1:1090091/1‑70 (MQ=255)
                                                             cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGa        >  1:1345052/1‑71 (MQ=255)
                                                               aCGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg          >  1:4638739/1‑67 (MQ=255)
                                                               aCGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg          >  1:2991026/1‑67 (MQ=255)
                                                               aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGTAACTGTATCAGGATCACCAg            <  1:325491/65‑1 (MQ=255)
                                                               aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGTAACTGTATCAGGATCACCAg            <  1:872409/65‑1 (MQ=255)
                                                               aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGAt       >  1:3082494/1‑70 (MQ=255)
                                                               aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATg      >  1:2006238/1‑71 (MQ=255)
                                                                cGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGc     <  1:3842395/71‑1 (MQ=255)
                                                                cGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGc     <  1:948531/71‑1 (MQ=255)
                                                                  ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                      <  1:2628966/52‑1 (MQ=255)
                                                                  ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                      <  1:3479341/52‑1 (MQ=255)
                                                                  ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                      <  1:4081904/52‑1 (MQ=255)
                                                                  ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGAt                  <  1:1430241/56‑1 (MQ=255)
                                                                    cACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt                                    <  1:2031250/36‑1 (MQ=255)
                                                                      |                                                                   
TCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTG  >  minE/834565‑834702

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