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 2,282,463 C→T 24.8% S289S (AGC→AGT)  sthA → pyridine nucleotide transhydrogenase, soluble

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,282,4630CT24.8% 153.9 / 41.2 120S289S (AGC→AGT) sthApyridine nucleotide transhydrogenase, soluble
Reads supporting (aligned to +/- strand):  ref base C (51/39);  new base T (12/18);  total (63/57)
Fisher's exact test for biased strand distribution p-value = 1.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 120 total aligned reads displayed.

CCAACGGTCGCACCGGTAATACCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTACGCGGTGGGC  >  minE/2282399‑2282526
                                                                |                                                               
ccAACGGTCGCACCGGTAATACCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCcgcg                                                             >  1:3350507/1‑69 (MQ=255)
 cAACGGTCGCACCGGTAATACCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCcgcg                                                             <  1:1909394/68‑1 (MQ=255)
           aCCGGTAATACCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAg                                                  <  1:577063/69‑1 (MQ=255)
                 aaTACCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAAc                                            >  1:1559975/1‑69 (MQ=255)
                    aCCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAg                                          >  1:207475/1‑68 (MQ=255)
                    aCCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAg                                          >  1:386604/1‑68 (MQ=255)
                    aCCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGc                                         >  1:983093/1‑69 (MQ=255)
                    aCCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGc                                         >  1:1942940/1‑69 (MQ=255)
                    aCCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGc                                         >  1:1817058/1‑69 (MQ=255)
                    aCCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGc                                         >  1:2217606/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:3138336/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:3125284/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:577187/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:2719383/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:2609803/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:2446948/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:2296181/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:630142/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:642735/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:713121/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        <  1:910484/69‑1 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:2003974/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:1123254/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:1472304/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        <  1:1573766/69‑1 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        <  1:1372550/69‑1 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:119065/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        <  1:1791002/69‑1 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:1819636/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:1923446/1‑69 (MQ=255)
                     ccGATTCGCTGGCGTTACAGAACAATGGGCTAGAAACTCACAGCCGCGGACAGCTGAAGGTCAACAGCa                                        >  1:366670/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTcgcg                                                             >  1:121680/1‑46 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCCACAGCAt                                       >  1:2244776/1‑68 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:3016988/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:2223692/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:691075/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:2352545/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:3343041/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:2974612/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:749776/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:3319323/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGATCAACAGCATg                                      >  1:3387132/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:2645496/1‑69 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCAtt                                      <  1:3122315/69‑2 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATg                                      <  1:2328867/69‑1 (MQ=255)
                       gATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATg                                      >  1:2017450/1‑69 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:2850878/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:722281/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:2769052/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:1953505/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:2719716/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:601959/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:3250217/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:1574590/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:24522/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:49989/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:2132150/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:2104173/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:1352220/67‑1 (MQ=255)
                        aTTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATg                                      <  1:777012/68‑1 (MQ=255)
                         ttCGCTGGCGTTACAGAACATTGGGCTGGAAACTGACAGTCGCGGACAGCTGAAGGTCAACAGCAt                                       <  1:1442045/66‑1 (MQ=255)
                                gCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGAc                              >  1:401456/1‑68 (MQ=255)
                                gCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGAc                              >  1:3109562/1‑68 (MQ=255)
                                gCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGAc                              >  1:2978637/1‑68 (MQ=255)
                                gCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGAc                              >  1:2873277/1‑68 (MQ=255)
                                gCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGAc                              >  1:2678597/1‑68 (MQ=255)
                                gCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGAc                              >  1:2552723/1‑68 (MQ=255)
                                gCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGAc                              >  1:631828/1‑68 (MQ=255)
                                gCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGAATCAGAc                              >  1:2209255/1‑68 (MQ=255)
                                    tACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGcac                         <  1:723578/69‑1 (MQ=255)
                                    tACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGcac                         <  1:851940/69‑1 (MQ=255)
                                    tACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGcac                         <  1:2361540/69‑1 (MQ=255)
                                    tACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGcac                         <  1:1234773/69‑1 (MQ=255)
                                     aCAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGcac                         <  1:864237/68‑1 (MQ=255)
                                           cATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCcaca                  >  1:2798382/1‑69 (MQ=255)
                                           cATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCcaca                  >  1:1349185/1‑69 (MQ=255)
                                           cATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCcaca                  >  1:129210/1‑69 (MQ=255)
                                             ttGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACg                <  1:68519/69‑1 (MQ=255)
                                             ttGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACg                <  1:202845/69‑1 (MQ=255)
                                              tGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACg                <  1:1762642/68‑1 (MQ=255)
                                                    aGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTAcgc         <  1:404260/69‑1 (MQ=255)
                                                    aGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTAcgc         <  1:3369881/69‑1 (MQ=255)
                                                    aGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTAcgc         <  1:3330413/69‑1 (MQ=255)
                                                    aGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTAcgc         <  1:3298825/69‑1 (MQ=255)
                                                    aGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTAcgc         <  1:2685456/69‑1 (MQ=255)
                                                    aGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTAcgc         <  1:2664898/69‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:84420/39‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   >  1:1104368/1‑39 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:311376/39‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:627786/39‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:1307995/39‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:572095/39‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   >  1:3321565/1‑39 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:3132747/39‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:2783228/39‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:2487736/39‑1 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   >  1:2304651/1‑39 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   >  1:1781874/1‑39 (MQ=255)
                                                        aCTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTAt                                   <  1:1961938/39‑1 (MQ=255)
                                                           gACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTACGCGGTGGGc  <  1:2799785/69‑1 (MQ=255)
                                                                |                                                               
CCAACGGTCGCACCGGTAATACCGATTCGCTGGCGTTACAGAACATTGGGCTAGAAACTGACAGCCGCGGACAGCTGAAGGTCAACAGCATGTATCAGACCGCACAGCCACACGTTTACGCGGTGGGC  >  minE/2282399‑2282526

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A