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 834,611 C→T 16.5% Y1023Y (TAC→TAT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE834,6110CT16.5% 208.2 / 29.2 91Y1023Y (TAC→TAT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (46/30);  new base T (8/7);  total (54/37)
Fisher's exact test for biased strand distribution p-value = 7.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

CAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATC  >  minE/834543‑834681
                                                                    |                                                                      
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACaa                                                                      >  1:913106/1‑71 (MQ=255)
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACa                                                                       <  1:19916/70‑1 (MQ=255)
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACa                                                                       <  1:3276936/70‑1 (MQ=255)
    cacaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGcc                                                                  >  1:5485810/1‑71 (MQ=255)
     gcaGCCGCGTAAAATTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGcgg                                                                 <  1:1426495/70‑3 (MQ=255)
     acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg                                                                 >  1:2810182/1‑71 (MQ=255)
     acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg                                                                 >  1:3431265/1‑71 (MQ=255)
     acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg                                                                 >  1:775879/1‑71 (MQ=255)
       aGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGt                                                               <  1:4438733/71‑1 (MQ=255)
       aGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGt                                                               <  1:3199465/71‑1 (MQ=255)
             gcAAAATTATCTCCAGCCCGCCCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTacac                                                          >  1:1316838/1‑70 (MQ=255)
             gcAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTacac                                                          >  1:4136311/1‑70 (MQ=255)
              taaaaTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACAcc                                                         >  1:2529333/2‑70 (MQ=255)
              cAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACa                                                                       >  1:1576026/1‑56 (MQ=255)
               aaaaTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCggg                                                                >  1:2979045/1‑62 (MQ=255)
                aaaTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAAc                                                      >  1:692219/1‑71 (MQ=255)
                 aaTTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACg                                                     >  1:5147618/1‑71 (MQ=255)
                   ttATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGtt                                                   <  1:4566101/71‑1 (MQ=255)
                      tctcCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCAc                                                >  1:422689/1‑71 (MQ=255)
                      tctcCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCAc                                                >  1:3109015/1‑71 (MQ=255)
                          cAGCCCGACCTGGTCTGGTCTGGAAGATGAACATGTTTCTTACAACGCCGGTTACACCAACGTTCAc                                                <  1:3874263/67‑1 (MQ=255)
                          cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAga                                            <  1:3325402/71‑2 (MQ=255)
                          cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGc                                            >  1:3771642/1‑71 (MQ=255)
                          cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGc                                            >  1:2279472/1‑71 (MQ=255)
                          cAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAgt                                            >  1:3245122/1‑70 (MQ=255)
                           aGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAgtt                                           <  1:3154329/71‑3 (MQ=255)
                               cGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGa                                              >  1:5564691/1‑64 (MQ=255)
                                 aCCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATcc                                      >  1:3053275/1‑70 (MQ=255)
                                  ccTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                    <  1:2859978/71‑1 (MQ=255)
                                   ctggtccggtCTGGAAAGCTATCACGTCTCCTATAACGCGGGATACACCAACGtt                                                   <  1:1773061/55‑1 (MQ=255)
                                   ctggtccggtCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGtt                                                   <  1:4670662/55‑1 (MQ=255)
                                    tggtctggtcTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATg                                  >  1:4345503/1‑71 (MQ=255)
                                      gtctggtctgGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTg                                          <  1:4221275/61‑1 (MQ=255)
                                      gtctggtctgGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGc                                >  1:1666562/1‑71 (MQ=255)
                                      gtccggtctgGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTgg                                 <  1:4443603/70‑1 (MQ=255)
                                        ctggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCg                               >  1:1296049/1‑70 (MQ=255)
                                        ccggtctggAAAGAGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGc                                >  1:2991480/3‑69 (MQ=255)
                                         tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                    <  1:997608/64‑1 (MQ=255)
                                         tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                    <  1:1082990/64‑1 (MQ=255)
                                         tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                    <  1:1249383/64‑1 (MQ=255)
                                         tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                    <  1:1256267/64‑1 (MQ=255)
                                          ggtctggAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCAc                            <  1:4005560/71‑1 (MQ=255)
                                           gtctggAAGATGAACACGTTTCTTACAACGCCGGTTaca                                                           >  1:4015644/1‑39 (MQ=255)
                                           gtctggAAGATGAACACGTTTCTTACAACGCCGGTTaca                                                           >  1:3717928/1‑39 (MQ=255)
                                           gtctggAAGATGAACACGTTTCTTACAACGCCGGTTa                                                             >  1:1806213/1‑37 (MQ=255)
                                           gtctggAAGATGAACACGTTTCTTACAACGCCGGTTa                                                             >  1:4715456/1‑37 (MQ=255)
                                           gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGt                              <  1:191628/68‑1 (MQ=255)
                                           gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTAc                            <  1:3967120/70‑1 (MQ=255)
                                           gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTAc                            <  1:4367756/70‑1 (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                      >  1:5173350/1‑71 (MQ=255)
                                                gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc                      <  1:1764458/71‑1 (MQ=255)
                                                gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc                      <  1:1157887/71‑1 (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)
                                                        acacGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGgtcgt               >  1:4333227/1‑70 (MQ=255)
                                                          acGTTTCTTACAACGCCGGTTACACCAACGTTCACGAg                                             >  1:4555694/1‑38 (MQ=255)
                                                          acGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAg            >  1:5009384/1‑71 (MQ=255)
                                                          acGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAg            <  1:266260/71‑1 (MQ=255)
                                                          acGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAg            >  1:1235246/1‑71 (MQ=255)
                                                           cGTTTCTTACAACGCCGGTTACACCAACGTTCACGAg                                             >  1:178022/1‑37 (MQ=255)
                                                           cGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAg            >  1:1435995/1‑70 (MQ=255)
                                                           cGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc           <  1:2199704/71‑1 (MQ=255)
                                                             tttCTTACAACGCCGGTTACACCAACTTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc           <  1:135404/69‑1 (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           >  1:2621404/1‑68 (MQ=255)
                                                              ttCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGc           >  1:2614700/1‑68 (MQ=255)
                                                               tCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                    >  1:3060372/1‑42 (MQ=255)
                                                               tCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                    >  1:174100/1‑42 (MQ=255)
                                                               tCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGc                          >  1:5035308/1‑52 (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                    >  1:2963754/1‑56 (MQ=255)
                                                                 ttACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                    >  1:1440838/1‑56 (MQ=255)
                                                                 ttACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg                    >  1:863518/1‑56 (MQ=255)
                                                                  tACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                                    <  1:1398375/39‑1 (MQ=255)
                                                                    cAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGc                                >  1:1838750/1‑41 (MQ=255)
                                                                    cAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGc                                >  1:2665952/1‑41 (MQ=255)
                                                                    cAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATc  <  1:3411846/71‑1 (MQ=255)
                                                                    |                                                                      
CAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATC  >  minE/834543‑834681

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