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
A7 F80 I2 R1 7 58.7 2928610 94.0% 2752893 132.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947 4,964,700 C→T E235K (GAA→AAA)  fleQ ← transcriptional regulator FleQ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,964,7000CT98.0% 162.8 / ‑4.4 50E235K (GAA→AAA) fleQtranscriptional regulator FleQ
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (23/26);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01

CGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTCGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGGCGCTTCGCGGCGCTTGGAATGGTAGTGCAGG  >  NC_002947/4964553‑4964845
                                                                                                                                                   |                                                                                                                                                 
ccatgatgCGCCCGTCGATGCTTTGTGTCTTGTTGCTACCCACGCGCTCTAAGGTACGCTCCTCCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCACGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGa                                                                                                                                                 <  2:357440/148‑1 (MQ=38)
         gcACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCgg                                                                                                                                        >  2:133877/1‑150 (MQ=255)
                  tGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTgg                                                                                                                               <  2:293226/150‑1 (MQ=255)
                   gCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGt                                                                                                                              <  2:992425/150‑1 (MQ=255)
                     tttGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGa                                                                                                                            >  2:914788/1‑150 (MQ=255)
                     tttGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGa                                                                                                                            >  2:166674/1‑150 (MQ=255)
                      ttGGGTCGGGTCGCTACCCCCCCGCTCGAAGGCACGGCCCTGCAGCACACGCATCATCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGAt                                                                                                                           <  2:606527/150‑1 (MQ=37)
                                       ccACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATg                                                                                                                          <  1:1406688/134‑1 (MQ=255)
                                       ccACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATg                                                                                                                          >  2:1406688/1‑134 (MQ=255)
                                       ccACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGgcgc                                                                                                          >  2:656235/1‑150 (MQ=255)
                                       ccACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGgcgc                                                                                                          <  1:166674/150‑1 (MQ=255)
                                        cACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGcc                                                                                                         >  1:496632/1‑150 (MQ=255)
                                        cACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGcc                                                                                                         <  1:914788/150‑1 (MQ=255)
                                            cgcTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTtc                                                                                                     <  2:1018236/150‑1 (MQ=255)
                                              cTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTtctc                                                                                                   <  1:656235/150‑1 (MQ=255)
                                                cGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGt                                                                                                 <  2:1234088/150‑1 (MQ=255)
                                                cGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGt                                                                                                 <  1:1379505/150‑1 (MQ=255)
                                                 gAAGGTACGCTCCTGCAGCACACGCAGCAGCTTTACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGAt                                                                                                                           >  2:750992/1‑123 (MQ=255)
                                                 gAAGGTACGCTCCTGCAGCACACGCAGCAGCTTTACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGAt                                                                                                                           <  1:750992/123‑1 (MQ=255)
                                                    ggTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTCGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGcc                                                                                             <  2:266900/150‑1 (MQ=255)
                                                      tACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCgc                                                                                           >  2:593921/1‑149 (MQ=255)
                                                         gCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTg                                                                                                                             <  1:73352/113‑1 (MQ=255)
                                                         gCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTg                                                                                                                             >  2:73352/1‑113 (MQ=255)
                                                                     cacGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCca                                                                            <  1:443224/150‑1 (MQ=255)
                                                                      acGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGc                                                                                                                                            <  2:1231767/85‑1 (MQ=255)
                                                                      acGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGc                                                                                                                                            >  1:1231767/1‑85 (MQ=255)
                                                                          agcagcTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCcagc                                                                          <  1:362135/147‑1 (MQ=255)
                                                                          agcagcTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCcagc                                                                          >  2:362135/1‑147 (MQ=255)
                                                                          agcagcTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCagcagc                                                                       >  1:1382518/1‑150 (MQ=255)
                                                                             agcTTGACCTGCATCGGCAACGGCATGTCGCCGATTTGTGCTAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCg                                                                    <  1:1401913/150‑1 (MQ=255)
                                                                                     cTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGAt                                                            >  2:69178/1‑150 (MQ=255)
                                                                                          tCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCgcgc                                                       <  2:496632/150‑1 (MQ=255)
                                                                                                 cGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGtt                                                <  2:1125599/150‑1 (MQ=255)
                                                                                                          gCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCAc                                       >  1:95801/1‑150 (MQ=255)
                                                                                                           ccGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCg                                                                    <  2:609738/120‑1 (MQ=255)
                                                                                                           ccGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCg                                                                    >  1:609738/1‑120 (MQ=255)
                                                                                                            cGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCCCGGCCGGGATCGCGCCACAGTTGACCGGCCCgc                                     >  2:413470/1‑149 (MQ=255)
                                                                                                               tttCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGG‑CCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGAc                                             <  1:310248/138‑1 (MQ=255)
                                                                                                               tttCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGG‑CCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGAc                                             >  2:310248/1‑138 (MQ=255)
                                                                                                                   gtcgAGGAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGgcgc                              >  2:603802/1‑150 (MQ=255)
                                                                                                                        ggAACAGGGTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGGCGCTTcgc                         >  1:1312277/1‑150 (MQ=255)
                                                                                                                                gTACCGCCGTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGGCGCTTCGCGGCGCTTg                 <  1:133877/150‑1 (MQ=255)
                                                                                                                                gTACCGCCGCTAGCCACTTTACCAGGCCAGTCACGGCTTGTTATTGCCCCGGTAAAGGCTCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGGCGCTTCGCGGCGCTTg                 <  2:13488/150‑1 (MQ=255)
                                                                                                                                     gccgTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCcaca                                                   <  2:662863/111‑1 (MQ=255)
                                                                                                                                     gccgTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCcaca                                                   >  1:662863/1‑111 (MQ=255)
                                                                                                                                      ccgTTGGCCAGTTTGAAGCGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGGCGCTTCGCGGCGCTTGGAATgg           >  1:264756/1‑150 (MQ=255)
                                                                                                                                      ccgTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGAGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGGTCGCGCCACAGTTGACCGGCACGAACGGCGCTTCGCGGCGCTTGGAATgg           >  1:472292/1‑150 (MQ=255)
                                                                                                                                       cgTTGGCCAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGAGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGGTCGCGCCACAGTTGACCCGCACGAACGGCGCTTCGCGGCGCTTGGAATGGt          <  2:472292/150‑1 (MQ=255)
                                                                                                                                              cAGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGGCGCTTCGCGGCGCTTGGAATGGTAGTGCAg   >  2:376206/1‑150 (MQ=255)
                                                                                                                                               aGTTTGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGGCGCTTCGCGGCGCTTGGAATGGTAGTGCAgg  <  1:69178/150‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                 
CGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTTGGCCAGTTCGAAACGCCCGGCACGGCTGGTGATGGCCCCGGTAAAGGCGCCCTTCTCGTGGCCGAACAGTTCGCTTTCCAGCAGCTCGGCCGGGATCGCGCCACAGTTGACCGGCACGAACGGCGCTTCGCGGCGCTTGGAATGGTAGTGCAGG  >  NC_002947/4964553‑4964845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A