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 2,606,682 G→A 32.8% R403R (CGC→CGT)  pitA ← phosphate transporter, low‑affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,606,6820GA32.8% 75.3 / 44.0 88R403R (CGC→CGT) pitAphosphate transporter, low‑affinity
Reads supporting (aligned to +/- strand):  ref base G (35/24);  new base A (9/20);  total (44/44)
Fisher's exact test for biased strand distribution p-value = 2.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.88e-01

Only 100 of 111 total aligned reads displayed.

GACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATA  >  minE/2606617‑2606750
                                                                 |                                                                    
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCAGCGATAGTCGTTGCCACACGgc                                                                     >  1:1863842/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGgc                                                                     >  1:1128436/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGgc                                                                     >  1:869297/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGgc                                                                     >  1:2721756/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGgc                                                                     >  1:3413255/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGgc                                                                     >  1:2894367/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGgc                                                                     >  1:202279/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGgc                                                                     >  1:3313561/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGgc                                                                     >  1:595347/1‑67 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGacgc                                                                   <  1:1061554/69‑1 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGacgc                                                                   <  1:218400/69‑1 (MQ=255)
gACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGacgc                                                                   <  1:3232928/69‑1 (MQ=255)
 aCATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGacgc                                                                   <  1:147560/68‑1 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:655438/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:1375470/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:1215440/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:1488954/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:435545/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:672947/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:3061293/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:2449846/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:3369615/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:1845/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCgccagcc                                                              >  1:2000575/1‑68 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCaccagcca                                                             >  1:1826995/1‑69 (MQ=255)
      cccTGAGCGTAGGTCATGCCTTTCTTACCGATTTTATCACCGATAGTCGTTGCCACACGGCgccagcca                                                             >  1:783486/1‑69 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:2247169/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:2747419/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:252071/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:2783101/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:710738/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:68469/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:3177301/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:2240971/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:1353177/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:367961/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:3347648/69‑1 (MQ=255)
             cGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:351320/69‑1 (MQ=255)
              gTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATCGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:1632224/68‑1 (MQ=255)
              gTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGt                                                     <  1:3049350/69‑1 (MQ=255)
              gTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGt                                                     <  1:1045971/69‑1 (MQ=255)
              gTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:1785235/68‑1 (MQ=255)
               tAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:3364050/67‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:573086/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:3365828/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:3112087/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:778779/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:2751482/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:1152551/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:249292/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:2435580/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:240038/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:1155572/69‑1 (MQ=255)
                    cATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGAt                                               <  1:1193737/69‑1 (MQ=255)
                        ccTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATAcc                                            >  1:1730951/1‑68 (MQ=255)
                        ccTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCt                                           >  1:74034/1‑69 (MQ=255)
                        ccTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCt                                           >  1:3309725/1‑69 (MQ=255)
                        ccTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCt                                           >  1:1369189/1‑69 (MQ=255)
                        ccTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCt                                           >  1:844388/1‑69 (MQ=255)
                        ccTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCt                                           >  1:2637564/1‑69 (MQ=255)
                        ccTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCt                                           >  1:870721/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTa                                                    >  1:2203228/1‑51 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:1189106/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:2723630/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:559885/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:552868/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:2147612/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:3286986/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:3067119/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:3068332/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:2336847/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAgc                                  >  1:2268511/1‑69 (MQ=255)
                                 ccGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAg                                   >  1:2374396/1‑68 (MQ=255)
                                       ttCTCACCGATAGTCGTTGCCACACGACGCCAGCCAATCATCg                                                      <  1:1835090/43‑1 (MQ=255)
                                                   gTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATc                <  1:2740229/69‑1 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:3189977/1‑69 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:2768888/1‑69 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:2865643/1‑69 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:1167832/1‑69 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:143045/1‑69 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:2139703/1‑69 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:391197/1‑69 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:3425538/1‑69 (MQ=255)
                                                        tGCCACACGACGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCacac           >  1:369295/1‑69 (MQ=255)
                                                             cacGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTg      <  1:1547312/69‑1 (MQ=255)
                                                             cacGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTg      <  1:2020784/69‑1 (MQ=255)
                                                             cacGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTg      <  1:1789249/69‑1 (MQ=255)
                                                             cacGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTg      <  1:1163531/69‑1 (MQ=255)
                                                             cacGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTg      <  1:1490821/69‑1 (MQ=255)
                                                               cGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCa    <  1:3148658/69‑1 (MQ=255)
                                                               cGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCa    <  1:513230/69‑1 (MQ=255)
                                                               cGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCa    <  1:451307/69‑1 (MQ=255)
                                                                 gcgcCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATa  <  1:1349066/69‑1 (MQ=255)
                                                                 gcgcCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATa  <  1:1715102/69‑1 (MQ=255)
                                                                 gcgcCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATa  <  1:584652/69‑1 (MQ=255)
                                                                 gcgcCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATa  <  1:765339/69‑1 (MQ=255)
                                                                 gcgcCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATa  <  1:419294/69‑1 (MQ=255)
                                                                 gcgcCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATa  <  1:78117/69‑1 (MQ=255)
                                                                 gcgcCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATa  <  1:330941/69‑1 (MQ=255)
                                                                 gcgcCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATa  <  1:3362348/69‑1 (MQ=255)
                                                                 |                                                                    
GACATCCCCTGAGCGTAGGTCATGCCTTTCTTACCGATTTTCTCACCGATAGTCGTTGCCACACGGCGCCAGCCAATCATCGTACCGATACCTAACGCCAGCGCGACCGCCATGATGATCCACACCGGTGCATA  >  minE/2606617‑2606750

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