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 1,934,245 G→A 22.2% I66I (ATC→ATT)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,934,2450GA22.2% 206.8 / 52.8 108I66I (ATC→ATT) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base G (40/44);  new base A (16/8);  total (56/52)
Fisher's exact test for biased strand distribution p-value = 1.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.13e-01

Only 100 of 109 total aligned reads displayed.

TGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTATGA  >  minE/1934177‑1934314
                                                                    |                                                                     
tGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGa                                                                      >  1:5539454/1‑70 (MQ=255)
     ggTAACGAAAGACGCTTTACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCa                                                                <  1:5377813/71‑1 (MQ=255)
        aaCGAAAGACGCTTTACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAgcg                                                             >  1:4978297/1‑71 (MQ=255)
           gAAAGACGCTTTACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCt                                                           >  1:2343918/1‑70 (MQ=255)
            aaaGACGCTTTACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTc                                                         >  1:3316697/1‑71 (MQ=255)
             aaGACGCTTTACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTcc                                                        <  1:2878285/71‑1 (MQ=255)
                aggCTTTCCCCATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGt                                                     <  1:4023622/69‑1 (MQ=255)
                 ggCTTTCCCCATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGtt                                                    >  1:4066856/2‑71 (MQ=255)
                  gCTTTCCCCATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGttt                                                                 <  1:2252670/57‑2 (MQ=255)
                  gCTTTCCCCATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGttc                                                   >  1:2613270/1‑71 (MQ=255)
                    tttCCCCATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGttcct                                                 >  1:3144320/1‑69 (MQ=255)
                    tttACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGtt                                                                  <  1:1295208/54‑1 (MQ=255)
                      tACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGttcttc                                                <  1:2759822/70‑1 (MQ=255)
                       aCCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCg                                               <  1:776813/70‑1 (MQ=255)
                        cccATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGttta                                                                >  1:3140687/1‑50 (MQ=255)
                        cccATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGttta                                                                >  1:5115961/1‑50 (MQ=255)
                         ccATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGttt                                                                 >  1:4348514/1‑49 (MQ=255)
                         ccATGATACGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGttt                                                                 >  1:4023336/1‑49 (MQ=255)
                          cATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGt                                                                   <  1:903255/47‑1 (MQ=255)
                          cATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCtt                                                          >  1:4280273/1‑56 (MQ=255)
                          cATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTtct                                           <  1:321230/71‑1 (MQ=255)
                          cATAATACGACGGGTCATCATGCGGCCAGCAACCGCGACTTCGATGt                                                                   <  1:4577549/47‑1 (MQ=255)
                            taataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTc                                                         <  1:2608632/55‑1 (MQ=255)
                            taataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTc                                                         <  1:2634463/55‑1 (MQ=255)
                            taataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTc                                                         <  1:2739660/55‑1 (MQ=255)
                            taataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGtt                                             <  1:1588650/67‑1 (MQ=255)
                            taataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTctct                                         >  1:2161738/1‑71 (MQ=255)
                             aataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCtt                                        >  1:740975/1‑71 (MQ=255)
                             aataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCtt                                        >  1:949985/1‑71 (MQ=255)
                              ataCGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGTTCCTGGTTATCctt                                       >  1:435370/1‑71 (MQ=255)
                              ataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGa                                                                      >  1:1455992/1‑40 (MQ=255)
                              ataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCttt                                       >  1:5287180/1‑71 (MQ=255)
                              ataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCttt                                       <  1:846781/71‑1 (MQ=255)
                              ataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCttt                                       >  1:2285625/1‑71 (MQ=255)
                              ataCGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCttt                                       >  1:3534875/1‑71 (MQ=255)
                               taCGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGTTCCTGGTTATCcttc                                      >  1:5462633/1‑70 (MQ=255)
                               taCGACGGGTCATCATTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGTTCCTGGTTATCcttc                                      >  1:666016/1‑70 (MQ=255)
                                 cgacgGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCa                                                       <  1:5205759/52‑1 (MQ=255)
                                 cgacgGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGcc                                    <  1:2983383/71‑1 (MQ=255)
                                 cgacgGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGc                                     <  1:3307086/70‑1 (MQ=255)
                                 cgacgGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGc                                     <  1:4796101/70‑1 (MQ=255)
                                     gggTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCg                                <  1:3866528/71‑1 (MQ=255)
                                       gTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGaa                              <  1:1442612/71‑1 (MQ=255)
                                         catcatGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGttctt                                                 <  1:1445814/50‑1 (MQ=255)
                                         catcatGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAAt                             >  1:618336/1‑70 (MQ=255)
                                          atcatTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGt                                                     <  1:4439579/45‑1 (MQ=255)
                                          atcatTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGTTCCTGGTTATCctt                                       >  1:555288/1‑59 (MQ=255)
                                          atcatTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGTTCCTGGTTATCctt                                       >  1:4256860/1‑59 (MQ=255)
                                           tcatGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTc                                                         <  1:2284141/40‑1 (MQ=255)
                                           tcatGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTc                                 <  1:3931232/64‑1 (MQ=255)
                                           tcatGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCt                          <  1:4701572/71‑1 (MQ=255)
                                           taatGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCttt                                       >  1:5677460/3‑58 (MQ=255)
                                            catTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGttcc                                                  <  1:5380309/46‑2 (MQ=255)
                                            catTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGttcc                                                  <  1:4904945/46‑2 (MQ=255)
                                            catTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGttcc                                                  <  1:4911708/46‑2 (MQ=255)
                                            catTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGttc                                                   >  1:4986892/1‑45 (MQ=255)
                                            catTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGttc                                                   >  1:1633243/1‑45 (MQ=255)
                                            catTCGGCCAGCAACCGAGACTTCAATGTTTAAGGATTCCAGttc                                                   >  1:4980481/1‑45 (MQ=255)
                                            catGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGa                               <  1:4416385/65‑1 (MQ=255)
                                            catGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTg                         >  1:4585570/1‑71 (MQ=255)
                                             atGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCg                                               >  1:5287455/1‑48 (MQ=255)
                                             atGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGtt                                             >  1:5369954/1‑50 (MQ=255)
                                             atGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTg                         <  1:923928/70‑1 (MQ=255)
                                             atGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTg                         <  1:4031458/70‑1 (MQ=255)
                                             atGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGc                        >  1:2425460/1‑71 (MQ=255)
                                             atGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCCTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTg                         <  1:4652666/70‑1 (MQ=255)
                                             atGAGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCg                                               >  1:4521076/1‑48 (MQ=255)
                                               gCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGt                      >  1:17456/1‑71 (MQ=255)
                                                 ggCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTg                     <  1:1099486/70‑1 (MQ=255)
                                                 ggCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGc                    <  1:3994730/71‑1 (MQ=255)
                                                   ccAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTg                                      <  1:5267452/51‑1 (MQ=255)
                                                   ccAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCaa                  >  1:48892/1‑71 (MQ=255)
                                                      gCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTg               >  1:714320/1‑71 (MQ=255)
                                                       cAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGaa                              >  1:2577827/1‑55 (MQ=255)
                                                       cAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGaa                              >  1:3238388/1‑55 (MQ=255)
                                                        aaCGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGt             <  1:807830/71‑1 (MQ=255)
                                                        aaCGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGt             >  1:3061736/1‑71 (MQ=255)
                                                        aaCGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGt             >  1:3421109/1‑71 (MQ=255)
                                                         aCGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGt             <  1:3417545/70‑1 (MQ=255)
                                                         aCGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTATGCGTGCAATTGGt             >  1:1375951/1‑70 (MQ=255)
                                                           ggCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCaa                  >  1:700856/1‑63 (MQ=255)
                                                           ggCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCaa                  >  1:1073703/1‑63 (MQ=255)
                                                           ggCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCaa                  >  1:3461357/1‑63 (MQ=255)
                                                            gCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGt             <  1:4214467/67‑1 (MQ=255)
                                                            gCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCa           >  1:851014/1‑69 (MQ=255)
                                                            gCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTATTTGCCGTCGAATTCTGCGCGCAATTGGTCa           >  1:1746159/1‑69 (MQ=255)
                                                              gACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAgg       >  1:4700983/1‑71 (MQ=255)
                                                               aCTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCag          <  1:5408656/67‑1 (MQ=255)
                                                               aCTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCag          <  1:2590850/67‑1 (MQ=255)
                                                               aCTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCag          <  1:2462445/67‑1 (MQ=255)
                                                                cTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTa     >  1:2552620/1‑71 (MQ=255)
                                                                cTTCAATGTTTAAGGATTCCAGTTCCTGGTTATCCTTCGCATCAAACTCTTCGTGCAACTGGTCAGAGGTa     <  1:3182353/71‑1 (MQ=255)
                                                                 ttCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGa                               <  1:5508224/44‑1 (MQ=255)
                                                                 ttCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCt                          <  1:1077842/49‑1 (MQ=255)
                                                                   cGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTAt    <  1:3968678/69‑1 (MQ=255)
                                                                   cGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTATg   >  1:3166334/1‑70 (MQ=255)
                                                                   cGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTATGa  >  1:3159777/1‑71 (MQ=255)
                                                                   cGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTATGa  >  1:874971/1‑71 (MQ=255)
                                                                   cGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTATGa  >  1:2747049/1‑71 (MQ=255)
                                                                    gATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTATGa  <  1:2304240/70‑1 (MQ=255)
                                                                    |                                                                     
TGCAGGGTAACGAAAGACGCTTTACCCATAATACGACGGGTCATCATGCGGCCAGCAACGGCGACTTCGATGTTCAGCGCTTCCAGTTCTTCGTTCTCTTTGCCGTCGAATTCTGCGTGCAATTGGTCAGAGGTATGA  >  minE/1934177‑1934314

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