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 2,612,173 T→C 47.3% K450K (AAA→AAG)  nikA ← nickel transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,612,1730TC47.3% 5.1 / 129.5 144K450K (AAA→AAG) nikAnickel transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (34/42);  new base C (30/38);  total (64/80)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.44e-01

Only 100 of 153 total aligned reads displayed.

CAGCGCCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTG  >  minE/2612107‑2612228
                                                                  |                                                       
cAGCGCCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGttt                                                       <  1:2937998/69‑1 (MQ=255)
cAGCGCCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGttt                                                       <  1:2805743/69‑1 (MQ=255)
cAGCGCCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGttt                                                       <  1:2664645/69‑1 (MQ=255)
cAGCGCCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGttt                                                       <  1:909232/69‑1 (MQ=255)
cAGCGCCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGttt                                                       <  1:2049976/69‑1 (MQ=255)
 aGCGCCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGttt                                                       <  1:1862257/68‑1 (MQ=255)
  gcgcCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGttt                                                       <  1:3220972/67‑1 (MQ=255)
              gCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCtt                                         >  1:1605930/1‑69 (MQ=255)
              gCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCtt                                         >  1:656987/1‑69 (MQ=255)
              gCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCtt                                         >  1:1727291/1‑69 (MQ=255)
              gCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCtt                                         >  1:1833000/1‑69 (MQ=255)
              gCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCtt                                         >  1:1335424/1‑69 (MQ=255)
                 tttCGTCATGGGTCGCGAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:1520391/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:1990788/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:2140861/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:3400185/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:252036/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:3025291/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:2928391/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:1434819/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:856164/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:1416129/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:1393721/68‑1 (MQ=255)
                 tttCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:954827/68‑1 (MQ=255)
                 tttCGTCATGGGGCGCGAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:1948370/68‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTaa                                              >  1:2390510/1‑59 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       >  1:911616/1‑66 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       <  1:1124352/66‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGc                                       >  1:1856561/1‑66 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:2320692/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:2361051/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:3090965/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:872679/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:2471009/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:1342975/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:784578/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:445762/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:1570026/67‑1 (MQ=255)
                   tCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCt                                      <  1:1509662/67‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:1144797/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:3358621/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:256070/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:3183318/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:226260/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:37215/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:2186253/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:925151/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:1813992/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:1647128/68‑1 (MQ=255)
                       cATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:558410/68‑1 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAg                       >  1:2308674/1‑67 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                      >  1:973603/1‑68 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                      >  1:486414/1‑68 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                      >  1:2671837/1‑68 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                      >  1:2670227/1‑68 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                      >  1:2212936/1‑68 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                      >  1:386616/1‑68 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                      >  1:2059906/1‑68 (MQ=255)
                                  aGCACTTCGCCGATCTCTTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGc                      >  1:1725121/1‑68 (MQ=255)
                                     aCTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCgtgt                  <  1:2622900/69‑1 (MQ=255)
                                     aCTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCgtgt                  <  1:2860625/69‑1 (MQ=255)
                                     aCTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCgtgt                  <  1:2824295/69‑1 (MQ=255)
                                        tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc               <  1:593548/69‑1 (MQ=255)
                                        tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc               <  1:437201/69‑1 (MQ=255)
                                        tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc               <  1:700254/69‑1 (MQ=255)
                                        tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc               <  1:1017639/69‑1 (MQ=255)
                                        tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc               <  1:3053585/69‑1 (MQ=255)
                                        tCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGAc               <  1:766930/69‑1 (MQ=255)
                                                ctctTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg       >  1:624490/1‑69 (MQ=255)
                                                ctctTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg       >  1:2969060/1‑69 (MQ=255)
                                                ctctTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg       >  1:1212179/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:3259197/42‑1 (MQ=38)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:2674647/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:1478589/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:545659/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:1550514/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:1461227/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:2169612/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:2428159/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:2461742/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:3280737/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:1105405/1‑69 (MQ=255)
                                                 tctTTATCAATCAGCGGCTTGTCGGCTAAACCTTGCTGTGCCTGGAAGTCAGCGTGCGACGGTACgcgc      >  1:142652/1‑69 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg       <  1:2188683/64‑1 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg       <  1:3013354/64‑1 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg       <  1:1055154/64‑1 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg       <  1:501918/64‑1 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTAcgcg       <  1:56316/64‑1 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCAtt   >  1:1028113/1‑68 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  >  1:1577264/1‑69 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  >  1:3408576/1‑69 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  >  1:3203085/1‑69 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  >  1:111457/1‑69 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  >  1:2750619/1‑69 (MQ=255)
                                                     tATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  >  1:2854327/1‑69 (MQ=255)
                                                     tATCAATCAGAGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  >  1:1147235/1‑69 (MQ=255)
                                                      atcaatcaGCGGCTTGTCGGCTAAACCTTGCTGTGcc                                 <  1:1264508/37‑1 (MQ=38)
                                                       tcaatcaGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  <  1:309528/67‑1 (MQ=255)
                                                       tcaatcaGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  <  1:2699194/67‑1 (MQ=255)
                                                       tcaatcaGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTg  <  1:2992150/67‑1 (MQ=255)
                                                                  |                                                       
CAGCGCCTGACGTTGCGTTTCGTCATGGGTCGCCAGCACTTCGCCGATCTCTTTATCAATCAGCGGTTTGTCGGCTAATCCTTGCTGTGCCTGGAAGTCAGCGTGTGACGGTACGCGCATTG  >  minE/2612107‑2612228

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