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
A16 F57 I0 R4 226 68.5 3221688 95.0% 3060603 125.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,723,822 A→G 100% S212S (TCA→TCG)  U712_19195 → putative transporter ywcJ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,723,8220AG100.0% 242.9 / ‑6.6 67S212S (TCA→TCG) U712_19195putative transporter ywcJ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (26/40);  minor base T (1/0);  total (27/40)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTGCCTCGCCTTTTTCATTCCAATGTCTCTTAAAGGGGAAGGGGCAAAGCTCTTTACCATGATGCTTTTCGTTTTCTGCTTCTTCATTTCCGGCTTCGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCACTTTTGATCGAGCACCCTGATACAGTGACAGTAATGGGAGCAGTCAGAAACTTAATTCCCGTTACACTCGGCAACCTGACCGCGGGAATGGTCATGATGGGCTGGATGTATTACACGCTCAAT  >  CP006881/3723686‑3723945
                                                                                                                                        |                                                                                                                           
tgtgCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCt                                                                                                                           >  7:19024/1‑139 (MQ=255)
  tgCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGGTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCttt                                                                                                                         >  7:396948/1‑139 (MQ=255)
     cTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATTCTATTCGATTTATGATTCTTTAATTCCGGCATTGAACAAACAAATGACAAAATGTTCACATTCGCCATCAAGCTTTTg                                                                                                                       >  4:44226/1‑138 (MQ=255)
     cTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGa                                                                                                                      >  3:21696/1‑139 (MQ=255)
     cTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGa                                                                                                                      >  6:307755/1‑139 (MQ=255)
       cGCCTTTTTCATTCCAATGTCACTCAAAGGCGAAGGAGCAAAGCTTTTTACCATGATGCTTGTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATc                                                                                                                    >  2:46410/1‑139 (MQ=255)
          cTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAg                                                                                                                 <  8:19024/139‑1 (MQ=255)
          cTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAg                                                                                                                 <  3:16833/139‑1 (MQ=255)
          cTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAg                                                                                                                 <  7:335637/139‑1 (MQ=255)
             tttCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCa                                                                                                               <  8:54274/138‑1 (MQ=255)
             tttCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCa                                                                                                               <  5:269046/138‑1 (MQ=255)
                  ttCCAATGTCTCTCAAAGGGGAAGGAGCATAGCATTTTACCATGATGCATTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAAAAAGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGa                                                                                                         <  5:82870/139‑1 (MQ=255)
                  ttCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGa                                                                                                         <  4:387584/139‑1 (MQ=255)
                       aTGTCTCTCAAAGGGTAAGGAGCATAGCTTTTTACCATGATGCTTTTCGTTTTCTTCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAg                                                                                                    <  3:44226/139‑1 (MQ=255)
                       aTGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAg                                                                                                    <  3:214786/139‑1 (MQ=255)
                          tctctcAAAGGGGAAGGAGCAAAGCTTTTTACAATGATGCTTTTCGTTTTCTGCTTCTTTATTTACGGCTTTTAACAAATCATTGCCAATAAGTACAAATTCGACATATATCTTTTTATCTAGCACAATGATACAGTGa                                                                                                 >  8:338065/1‑139 (MQ=255)
                             ctcaaaGGGGAAGGAGCAAAGCGTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGATTTTGATCGAGCACCCTCATACAGTGACac                                                                                              >  3:347179/4‑138 (MQ=255)
                              tctaaggggaaggagCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               <  8:138461/134‑1 (MQ=255)
                              tcaaaGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               <  5:135379/135‑1 (MQ=255)
                              tcaaaGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATAAGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               <  1:124220/135‑1 (MQ=255)
                                  aggggaaggagCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               <  7:319875/133‑1 (MQ=255)
                                  aggggaaggagCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               >  8:319875/1‑133 (MQ=255)
                                      gaaggagCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAg                                                                                     <  5:49511/139‑1 (MQ=255)
                                              aaaGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGa                                                                             <  4:21696/139‑1 (MQ=255)
                                              aaaGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGa                                                                             <  5:158524/139‑1 (MQ=255)
                                                     tttACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTaa                                                                      >  3:269693/1‑139 (MQ=255)
                                                       tACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAAt                                                                     <  7:202287/138‑1 (MQ=255)
                                                            tgatgCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGa                                                                                                         <  3:247793/97‑1 (MQ=255)
                                                            tgatgCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGa                                                                                                         <  1:367912/97‑1 (MQ=255)
                                                            tgatgCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGa                                                                                                         >  4:247793/1‑97 (MQ=255)
                                                            tgatgCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGa                                                                                                         >  2:367912/1‑97 (MQ=255)
                                                            tgatgCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGt                                                               >  4:317369/1‑139 (MQ=255)
                                                            tgatgCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGt                                                               >  5:159786/1‑139 (MQ=255)
                                                                                  ctttATTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACcgcg                                         >  4:151475/1‑139 (MQ=255)
                                                                                     taTTTCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCggg                                       <  2:277068/137‑1 (MQ=255)
                                                                                       tttCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGGACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTTCGCTCGGCAATCTGACCGCGGGaa                                     <  1:46410/138‑1 (MQ=255)
                                                                                       tttCCGGCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATAGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGaa                                     <  6:159786/138‑1 (MQ=255)
                                                                                            ggCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAg                                                                              <  5:243643/92‑1 (MQ=255)
                                                                                            ggCTTTGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAg                                                                              >  6:243643/1‑92 (MQ=255)
                                                                                              cTTTGAACACAGCATTGACAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTatg                             <  8:396948/139‑1 (MQ=255)
                                                                                                   aaCACAGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATggg                        <  4:347179/139‑1 (MQ=255)
                                                                                                     cacaTCATTGCCTATATGTGCACATTCTCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCt                      <  7:338065/139‑1 (MQ=255)
                                                                                                     cacaGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCt                      <  1:260799/139‑1 (MQ=255)
                                                                                                     cacaGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCt                      <  4:269693/139‑1 (MQ=255)
                                                                                                       caGCATTGCCTATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                    <  3:317369/139‑1 (MQ=255)
                                                                                                       caGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                    <  5:307755/139‑1 (MQ=255)
                                                                                                       caGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                    <  3:151475/139‑1 (MQ=255)
                                                                                                       caGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTg                     >  7:390974/1‑138 (MQ=255)
                                                                                                         gCATTGACAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGAt                  <  6:42779/139‑1 (MQ=255)
                                                                                                            ttGCCAATCTGTGCACATTCGCCAGCTCGCGTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTa               <  8:340813/139‑1 (MQ=255)
                                                                                                             tGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAg                                                                                                                 >  2:287010/1‑40 (MQ=255)
                                                                                                             tGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAg                                                                                                                 <  1:287010/40‑1 (MQ=255)
                                                                                                             tGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAg                                                                                                    >  3:151465/1‑53 (MQ=255)
                                                                                                             tGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAg                                                                                                    <  4:151465/53‑1 (MQ=255)
                                                                                                                  atatGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGAt                  >  8:238013/1‑130 (MQ=255)
                                                                                                                  atatGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGAt                  <  7:238013/130‑1 (MQ=255)
                                                                                                                    atGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               <  6:89486/51‑1 (MQ=255)
                                                                                                                    atGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               >  5:89486/1‑51 (MQ=255)
                                                                                                                        gCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGaa   >  5:162441/1‑139 (MQ=255)
                                                                                                                         cacaTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               >  4:169050/1‑46 (MQ=255)
                                                                                                                         cacaTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACa                                                                                               <  3:169050/46‑1 (MQ=255)
                                                                                                                         cacaTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                    >  1:116100/1‑121 (MQ=255)
                                                                                                                         cacaTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                    <  2:116100/121‑1 (MQ=255)
                                                                                                                         cacaTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAAt  >  7:345228/1‑139 (MQ=255)
                                                                                                                         cacaTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAAt  >  3:268857/1‑139 (MQ=255)
                                                                                                                                 ccATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATgg                         >  8:136955/1‑108 (MQ=255)
                                                                                                                                 ccATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATgg                         <  7:136955/108‑1 (MQ=255)
                                                                                                                                        |                                                                                                                           
TGTGCCTCGCCTTTTTCATTCCAATGTCTCTTAAAGGGGAAGGGGCAAAGCTCTTTACCATGATGCTTTTCGTTTTCTGCTTCTTCATTTCCGGCTTCGAACACAGCATTGCCAATATGTGCACATTCGCCATCTCACTTTTGATCGAGCACCCTGATACAGTGACAGTAATGGGAGCAGTCAGAAACTTAATTCCCGTTACACTCGGCAACCTGACCGCGGGAATGGTCATGATGGGCTGGATGTATTACACGCTCAAT  >  CP006881/3723686‑3723945

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