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
A26 F57 I1 R1 119 93.8 3687158 95.5% 3521235 127.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 3,724,831 C→T intergenic (‑5/+35) U712_19200 ← / ← U712_19205 SacPA operon antiterminator/Uncharacterized protein ywcI

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,724,8310CT100.0% 169.9 / NA 58intergenic (‑5/+35)U712_19200/U712_19205SacPA operon antiterminator/Uncharacterized protein ywcI
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/32);  total (26/32)

TTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTATCTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCAGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGCGCGG  >  CP006881/3724695‑3724963
                                                                                                                                        |                                                                                                                                    
ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                                                                                                                                    >  8:88885/1‑139 (MQ=255)
ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                                                                                                                                    >  7:70117/1‑139 (MQ=255)
              tAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAAt                                                                                                                      <  7:88885/139‑1 (MQ=255)
               aGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGTTTATCTCTCCCGCCAttt                                                                                                                     >  2:167643/1‑139 (MQ=255)
                gggATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACCATATATTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCACCCGCCAAtt                                                                                                                     >  5:118670/1‑138 (MQ=255)
                    tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGATGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt                                                                                                                >  4:153926/1‑139 (MQ=255)
                    tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCAGGTCCCATCACGATTTTTTACTGATCATAGTCTTTTATTAAAGCCGCATTGTTTTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCACGCAAATTAGCtg                                                                                                                >  5:305360/1‑138 (MQ=255)
                     gatttCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt                                                                                                                <  6:73435/134‑1 (MQ=255)
                         tCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGAc                                                                                                           <  3:1929/139‑1 (MQ=255)
                           aTTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGGATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTg                                                                                                         >  6:274790/1‑139 (MQ=255)
                           aTTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTg                                                                                                         >  2:382185/1‑139 (MQ=255)
                                     ttttGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTAc                                                                                                <  5:412104/138‑1 (MQ=255)
                                     ttttGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGATGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTAc                                                                                                <  3:153926/138‑1 (MQ=255)
                                                 aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                   <  2:152263/139‑1 (MQ=255)
                                                 aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                   <  8:292683/139‑1 (MQ=255)
                                                 aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                   <  3:218912/139‑1 (MQ=255)
                                                 aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                   <  8:70117/139‑1 (MQ=255)
                                                 aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                   <  4:350893/139‑1 (MQ=255)
                                                 aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                   <  3:96097/139‑1 (MQ=255)
                                                        gTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGt                                                                             >  6:157149/1‑138 (MQ=255)
                                                         tCCCATCACGATTTTTTCCTGATCTTCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTa                                                                            >  7:109840/1‑138 (MQ=255)
                                                              tCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTATCCCGCCCATTTGCTTTTGACTGTGATTTTACCTCCTTTTGACCGCCATGGAAACATg                                                                      >  1:218250/1‑139 (MQ=255)
                                                                   aTTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGc                                                                 <  8:235894/139‑1 (MQ=255)
                                                                       tttCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACt                                                                                                          >  8:144886/1‑94 (MQ=255)
                                                                       tttCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACt                                                                                                          <  7:144886/94‑1 (MQ=255)
                                                                         tCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGcccg                                                              >  8:414455/1‑134 (MQ=255)
                                                                         tCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGcccg                                                              <  7:414455/136‑3 (MQ=255)
                                                                         tCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGct                                                            <  5:157149/138‑1 (MQ=255)
                                                                         tCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGct                                                            <  7:45313/138‑1 (MQ=255)
                                                                              atcatcCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCtctctc                                                       <  3:363/138‑1 (MQ=255)
                                                                                  tcCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCt                                                  <  7:192169/139‑1 (MQ=255)
                                                                                   ccTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGcgt                                                 >  4:254086/1‑137 (MQ=255)
                                                                                   ccTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACATCCTATTGACCGCCATGTAAAGAAGCGGGCCCGCGCTCTCCTGCta                                                 >  7:89362/1‑138 (MQ=255)
                                                                                          tattaAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCATGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGa                                           <  4:289469/138‑1 (MQ=255)
                                                                                          tattaAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGa                                           <  1:382185/138‑1 (MQ=255)
                                                                                          tattaAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGa                                           <  7:454433/138‑1 (MQ=255)
                                                                                          tattaAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGa                                           <  6:368030/138‑1 (MQ=255)
                                                                                          tattaAAGCCGCATTGTTGGTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGa                                           <  2:137006/138‑1 (MQ=255)
                                                                                          tattaAAGCCGCATTGTTGGTTAATACTTTATAGAGTTTCAAGAGGTTATCTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGa                                           <  8:316904/138‑1 (MQ=255)
                                                                                                 gCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTg                                    >  1:139475/1‑138 (MQ=255)
                                                                                                     cATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGc                               <  3:58531/139‑1 (MQ=255)
                                                                                                     cATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGc                               >  5:138853/1‑139 (MQ=255)
                                                                                                            gttTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCaa                         <  6:36297/138‑1 (MQ=255)
                                                                                                               taatACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAATATGCGGGCCCGCGCTGTCCTGCTTTGGCGATTCCTTGAAGGCTTGCTAACAt                     >  3:245098/4‑139 (MQ=255)
                                                                                                                    cTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACAtcttct                >  7:280610/1‑139 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                   <  6:26141/69‑1 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                   >  5:26141/1‑69 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGcc                                                                                 <  6:178326/71‑1 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGcc                                                                                 >  5:178326/1‑71 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATg                                                                      <  2:5720/82‑1 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATg                                                                      >  1:5720/1‑82 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCa                          >  2:268426/1‑126 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCa                          <  1:268426/126‑1 (MQ=255)
                                                                                                                       tataGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACAtcttagttt             >  1:426431/1‑134 (MQ=255)
                                                                                                                           gATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTtata          <  3:346162/138‑1 (MQ=255)
                                                                                                                              tttCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAgc      >  2:291701/1‑139 (MQ=255)
                                                                                                                               ttCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAgcg     >  8:301927/1‑139 (MQ=255)
                                                                                                                                  aaGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGCgcgg  <  5:274790/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                    
TTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTATCTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCAGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGCGCGG  >  CP006881/3724695‑3724963

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A