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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,612,185 T→A 45.6% G446G (GGA→GGT)  nikA ← nickel transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,612,1850TA45.6% 41.9 / 166.4 149G446G (GGA→GGT) nikAnickel transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (34/47);  new base A (30/38);  total (64/85)
Fisher's exact test for biased strand distribution p-value = 8.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 149 total aligned reads displayed.

GCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTGAACTGAGGAAGGCGTGTGGATCA  >  minE/2612121‑2612251
                                                                |                                                                  
gCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCtt                                                                >  1:9646/1‑69 (MQ=255)
gCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCtt                                                                >  1:1605930/1‑69 (MQ=255)
gCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCtt                                                                >  1:1335424/1‑69 (MQ=255)
   tttCGTCATGGGTCGCGAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:1520391/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:3271888/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:252036/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:2928391/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:1990788/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:3025291/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:3058307/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:3400185/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:425787/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:1434819/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:1416129/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:1393721/68‑1 (MQ=255)
   tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:1129454/68‑1 (MQ=255)
   tttCGTCATGGGGCGCGAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:1948370/68‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              >  1:1856561/1‑66 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              <  1:1124352/66‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:2471009/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:2320692/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:2250279/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:2837688/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:2166849/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:872679/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:784578/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:1342975/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:1570026/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:1509662/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                                             <  1:589716/67‑1 (MQ=255)
     tCGTCATGGGTCGCCAGCACTTCGCAGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                                              >  1:3368608/1‑66 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:3204441/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:925151/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:256070/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:2311954/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:226260/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:54650/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:37215/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:2917336/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:1813992/68‑1 (MQ=255)
         cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCAGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:2599749/68‑1 (MQ=255)
            gggTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:1663811/65‑1 (MQ=255)
             ggTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGaa                                                   >  1:822466/1‑69 (MQ=255)
                    aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                                             >  1:2671837/1‑68 (MQ=255)
                    aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                                             >  1:2670227/1‑68 (MQ=255)
                    aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                                             >  1:751790/1‑68 (MQ=255)
                    aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                                             >  1:973603/1‑68 (MQ=255)
                    aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                                             >  1:3135868/1‑68 (MQ=255)
                    aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                                             >  1:486414/1‑68 (MQ=255)
                    aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                                             >  1:2059906/1‑68 (MQ=255)
                    aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                                             >  1:1725121/1‑68 (MQ=255)
                       aCTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCgtgt                                         <  1:1111360/69‑1 (MQ=255)
                       aCTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCgtgt                                         <  1:2824295/69‑1 (MQ=255)
                          tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc                                      <  1:437201/69‑1 (MQ=255)
                          tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc                                      <  1:3053585/69‑1 (MQ=255)
                          tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc                                      <  1:2059031/69‑1 (MQ=255)
                          tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc                                      <  1:1768181/69‑1 (MQ=255)
                          tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc                                      <  1:700254/69‑1 (MQ=255)
                          tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc                                      <  1:2187824/69‑1 (MQ=255)
                          tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc                                      <  1:1017639/69‑1 (MQ=255)
                                  ctctTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg                              >  1:624490/1‑69 (MQ=255)
                                  ctctTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg                              >  1:1212179/1‑69 (MQ=255)
                                  ctctTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg                              >  1:2969060/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:1478589/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:1550514/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:2428159/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:3280737/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:1461227/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:142652/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:545659/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:641414/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:1105405/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:880155/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:92005/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:2461742/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:2674647/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:1850724/1‑69 (MQ=255)
                                   tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc                             >  1:2169612/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg                              <  1:2188683/64‑1 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg                              <  1:3013354/64‑1 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg                              <  1:56316/64‑1 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCAtt                          >  1:1028113/1‑68 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:2372010/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:2625111/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:2750619/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:1577264/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:2854327/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:1445043/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:347573/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:3203085/1‑69 (MQ=255)
                                       tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTCTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:478230/1‑69 (MQ=255)
                                       tATCAATCAGAGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         >  1:1147235/1‑69 (MQ=255)
                                        atcaatcaGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                                        <  1:1264508/37‑1 (MQ=38)
                                         tcaatcaGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         <  1:2992150/67‑1 (MQ=255)
                                         tcaatcaGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         <  1:2699194/67‑1 (MQ=255)
                                         tcaatcaGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg                         <  1:309528/67‑1 (MQ=255)
                                                              aaTCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTGAACTGAGGAAGGCGTGTGGATCa  <  1:2848117/69‑1 (MQ=255)
                                                              aaTCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTGAACTGAGGAAGGCGTGTGGATCa  <  1:1043304/69‑1 (MQ=255)
                                                              aaTCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTGAACTGAGGAAGGCGTGTGGATCa  <  1:1176414/69‑1 (MQ=255)
                                                              aaTCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTGAACTGAGGAAGGCGTGTGGATCa  <  1:1638731/69‑1 (MQ=255)
                                                                |                                                                  
GCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTGAACTGAGGAAGGCGTGTGGATCA  >  minE/2612121‑2612251

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