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
A18 F53 I0 R2 221 66.0 2680176 94.9% 2543487 126.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,724,719 G→A 100% D36D (GAC→GAT)  U712_19200 ← SacPA operon antiterminator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,724,7190GA100.0% 197.8 / NA 61D36D (GAC→GAT) U712_19200SacPA operon antiterminator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/26);  total (35/26)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CATAGCTGATGATATCCTCAGCTATTTCAATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTAAACTTTTCATTCTCGTCGTGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTATCTCTCCCGCCAATTAGCTT  >  CP006881/3724595‑3724853
                                                                                                                            |                                                                                                                                      
cATAGCTGATGATATCCTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCttttt                                                                                                                          >  3:273885/1‑139 (MQ=255)
  tAGCTGATGATATCCTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCttttttt                                                                                                                        >  1:81615/1‑139 (MQ=255)
    gCTGATGATATCCTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTg                                                                                                                       >  6:160685/1‑138 (MQ=255)
        atgatATCCTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAg                                                                                                                  >  6:230171/1‑139 (MQ=255)
        atgatATCCTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAg                                                                                                                  >  4:125993/1‑139 (MQ=255)
             atCCTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGGAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGAtt                                                                                                             >  1:89308/1‑139 (MQ=255)
               ccTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTcc                                                                                                           >  8:78913/1‑139 (MQ=255)
               ccTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTcc                                                                                                           >  4:36937/1‑139 (MQ=255)
               ccTCAGCAATTTCTATAAGCTCCTCCGGCAGTGTTTGCACGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTATATTCATTCGGAAGAGATCAGTTTTCTTTTTTTGAAAAGCGATTcc                                                                                                           >  5:168278/1‑139 (MQ=255)
                cTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTcc                                                                                                           <  6:258304/138‑1 (MQ=255)
                   aGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGt                                                                                                       >  7:257709/1‑139 (MQ=255)
                   aGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGt                                                                                                       >  2:287925/1‑139 (MQ=255)
                        tttCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCAt                                                                                                  >  4:9868/1‑139 (MQ=255)
                           ctatatGCTCCTCCGGCAGTGATTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCTCGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCa                                                                                                <  6:168278/136‑1 (MQ=255)
                                tGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGTATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGAttt                                                                                          >  1:200111/1‑139 (MQ=255)
                                  ctcctcCGGCAGTGTTTGCAGGATTTGTTTGCAGTTTGCATTGTCGTCGCGCCCGCCAAAGATCTTTTCCCCTTTTTTCTTTGGGAGGAGAGCATTTTTCTTTTTTTGAAAGGCGATTCCCGGGCCCAGCACGAttttt                                                                                        >  6:287798/1‑139 (MQ=255)
                                  ctcctcCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGAttttt                                                                                        >  5:304239/1‑139 (MQ=255)
                                    cctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTc                                                                                      >  1:252401/1‑139 (MQ=255)
                                     ctccTGGAGTGTTTGCAGGATTTGTTTGAAATTTTCATTCTCGTAGCGCACGACAAAGATATTTTCCAATTTATTAATCGTGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACTATTTTTTcg                                                                                     <  2:47865/139‑2 (MQ=255)
                                     ctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                     >  3:11853/1‑139 (MQ=255)
                                     ctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                     >  8:259006/1‑139 (MQ=255)
                                     ctccGGCAGTGTTTGCACGATTTGTTTGAACTTTTCATTCTCTTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCAATTTTCTATTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTAcc                                                                                     >  8:207043/1‑139 (MQ=255)
                                     ctccGGCAGTGGTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTc                                                                                      <  7:78913/138‑1 (MQ=255)
                                      tccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCt                                                                                    >  6:19056/1‑139 (MQ=255)
                                      tccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCt                                                                                    >  6:99240/1‑139 (MQ=255)
                                             gtgtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcatc                                                                             >  7:226923/1‑139 (MQ=255)
                                             gtgtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcatc                                                                             <  5:28024/139‑1 (MQ=255)
                                              tgtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATcc                                                                            <  3:9868/139‑1 (MQ=255)
                                               gtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCct                                                                           >  6:183128/1‑139 (MQ=255)
                                               gtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTCTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCct                                                                           >  1:38075/1‑139 (MQ=255)
                                                  tGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCctct                                                                         <  2:81615/138‑1 (MQ=255)
                                                  tGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCctct                                                                         <  4:62576/138‑1 (MQ=255)
                                                       gATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTttatt                                                                   <  8:257709/139‑1 (MQ=255)
                                                        aTTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTttatt                                                                   >  1:137019/1‑138 (MQ=255)
                                                        aTTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTttatt                                                                   >  6:187194/1‑138 (MQ=255)
                                                            gTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAg                                                               <  8:226923/138‑1 (MQ=255)
                                                            gTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGc                                                              >  6:145662/1‑139 (MQ=255)
                                                                 acattttCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCACTTCCCGGTCCCATCACGATTTTTTCCTGATGATCATCTTTTATTAAAGCCGCAt                                                         >  1:8967/4‑139 (MQ=255)
                                                                   cTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATTGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGTTTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCAttg                                                       <  3:248449/139‑1 (MQ=255)
                                                                   cTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCAttg                                                       <  5:103539/139‑1 (MQ=255)
                                                                   cTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCAttg                                                       <  7:259006/139‑1 (MQ=255)
                                                                   cTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCAttg                                                       <  5:183128/139‑1 (MQ=255)
                                                                   cTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAAGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCAttg                                                       <  7:326830/139‑1 (MQ=255)
                                                                          ttCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTa                                                <  2:200111/139‑1 (MQ=255)
                                                                          ttCTCGGCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTa                                                <  5:327133/139‑1 (MQ=255)
                                                                            ctcGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTaa                                               <  8:186925/138‑2 (MQ=255)
                                                                            ctcGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTaa                                               <  5:160685/138‑2 (MQ=255)
                                                                               gtcgcGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTaat                                              <  2:252401/136‑3 (MQ=255)
                                                                                     cACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAg                                     <  3:36937/139‑1 (MQ=255)
                                                                                         aCAAAGATCTTTTCCACTTTATTAATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGAAAATCCTCATTTATTTAAGCCGCAATGTTGTTTAAAACTTTATAGAttt                                 >  8:236807/1‑139 (MQ=255)
                                                                                            aaGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCa                              <  6:42217/139‑1 (MQ=255)
                                                                                             aGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCaa                             <  2:137019/139‑1 (MQ=255)
                                                                                                  ttttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAggt                        >  4:272828/1‑138 (MQ=255)
                                                                                                         cTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAtctct                 >  6:315864/1‑139 (MQ=255)
                                                                                                            tATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTccc              >  6:301571/1‑139 (MQ=255)
                                                                                                                  tAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAAt        <  4:171977/139‑1 (MQ=255)
                                                                                                                   aGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcatc                                                                             >  6:192976/1‑69 (MQ=255)
                                                                                                                   aGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcatc                                                                             <  5:192976/69‑1 (MQ=255)
                                                                                                                        tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt  >  7:1004/1‑139 (MQ=255)
                                                                                                                        tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt  >  7:195486/1‑139 (MQ=255)
                                                                                                                        tGAGATCATTCTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt  <  2:38075/139‑1 (MQ=255)
                                                                                                                            |                                                                                                                                      
CATAGCTGATGATATCCTCAGCTATTTCAATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTAAACTTTTCATTCTCGTCGTGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTATCTCTCCCGCCAATTAGCTT  >  CP006881/3724595‑3724853

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