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 I0 R1 1148 65.4 3296958 93.8% 3092546 131.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,162,148 T→A 20.2% intergenic (‑48/+29) PP_3663 ← / ← pssA GGDEF domain‑containing protein/CDP‑diacylglycerol‑‑serine O‑phosphatidyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,162,1480TA20.2% 115.3 / 23.3 49intergenic (‑48/+29)PP_3663/pssAGGDEF domain‑containing protein/CDP‑diacylglycerol‑‑serine O‑phosphatidyltransferase
Reads supporting (aligned to +/- strand):  ref base T (18/21);  new base A (6/4);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 4.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCCGACTGTATGCGATCGTGATCACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTGCCGAACCGATTCTCGGC  >  NC_002947/4161999‑4162297
                                                                                                                                                      |                                                                                                                                                     
gCCCGACTGTATGCGATCGTGATCACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCtt                                                                                                                                                       <  1:537462/150‑1 (MQ=255)
  ccGACTGTATGCGATCGTGATCACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGc                                                                                                                                                     >  2:798879/1‑150 (MQ=255)
          aTGCGATCGTGATCACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCCGGCAAGCCAGCGACa                                                                                                                                             <  2:4240/150‑1 (MQ=255)
            gCGATCGTGATCACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAgg                                                                                                                                           <  2:503521/150‑1 (MQ=255)
               aTCGTGATCACGTTCAGAGGGGCATTGCACTGTTACCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCCGCAATATCATAATGAAATCAATG‑CGCGGTGAGCACCACTCTGGCACTGCCGCAGGCTACCCGGCGACAGGGTc                                                                                                                                        >  2:428476/1‑150 (MQ=255)
                      tCACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAg                                                                                                                                 >  1:526366/1‑150 (MQ=255)
                       cACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAgg                                                                                                                                <  1:1224418/150‑1 (MQ=255)
                       cACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAgg                                                                                                                                <  1:798879/150‑1 (MQ=255)
                                agGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCCATG‑AAATGTTGAATATGCACAGTCACGTTCGCTGGCTTGCCGGCGACAGGGCCAGTACGCGCTATGTCag                                                                                                                       >  1:1012427/1‑150 (MQ=255)
                                 ggggCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCaga                                                                                                                      <  2:1462821/150‑1 (MQ=255)
                                 ggggCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCaga                                                                                                                      <  2:1542276/150‑1 (MQ=255)
                                    gCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATGCCGCCG‑ACGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCa                                                                                                                   >  1:920292/1‑150 (MQ=255)
                                      cTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAGAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCAcc                                                                                                                 >  1:1568791/1‑150 (MQ=255)
                                                         aTTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCa                                                                                              >  1:213348/1‑150 (MQ=255)
                                                            gTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAAcc                                                                                           <  1:317272/150‑1 (MQ=255)
                                                                tCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCt                                                                                       >  2:1345106/1‑150 (MQ=255)
                                                                   aGCCCCTGACAAAGGGTCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCtata                                                                                    >  2:1048095/1‑150 (MQ=255)
                                                                   aGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCtata                                                                                    <  1:428476/150‑1 (MQ=255)
                                                                   aGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCtata                                                                                    >  2:1568594/1‑150 (MQ=255)
                                                                             aaaGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAgg                                                                                                                                <  1:1622784/96‑1 (MQ=255)
                                                                             aaaGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAgg                                                                                                                                >  2:1622784/1‑96 (MQ=255)
                                                                               aGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAAc                                                                             >  1:1542070/1‑145 (MQ=255)
                                                                               aGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAAc                                                                             <  2:1542070/145‑1 (MQ=255)
                                                                                      tGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAAc                                                                 <  2:213348/150‑1 (MQ=255)
                                                                                      tGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTCTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGAGCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAAc                                                                 <  1:1568594/150‑1 (MQ=255)
                                                                                        ggCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCCAACGGCTATAGCGCAACCGTTGCAGAAACtt                                                               <  2:920292/150‑1 (MQ=255)
                                                                                          cagcaATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTgc                                                             <  2:526366/150‑1 (MQ=255)
                                                                                          cagcaATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTgc                                                             <  1:1048095/150‑1 (MQ=255)
                                                                                            gcaATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTgcgc                                                           >  1:551645/1‑150 (MQ=255)
                                                                                                  tCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCActtgc                                                     >  2:921327/1‑150 (MQ=255)
                                                                                                               aaTG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGt                                                                                                                                         >  2:1133450/1‑53 (MQ=255)
                                                                                                               aaTG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGt                                                                                                                                         <  1:1133450/53‑1 (MQ=255)
                                                                                                               aaTG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCgg                                        <  1:1173062/150‑1 (MQ=255)
                                                                                                               aaTG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCgg                                        >  1:1233174/1‑150 (MQ=255)
                                                                                                                 tG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGATTGGGATGTTCGGcc                                      >  2:688494/1‑150 (MQ=255)
                                                                                                                      cgGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTtct                                  <  2:1568791/150‑1 (MQ=255)
                                                                                                                                     tgacccTGTCGCCGGCAAGCCAGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTg                   >  2:1450678/4‑150 (MQ=255)
                                                                                                                                     tgacccTGTCGCCGGCAAGCCAGCGACAGGGCCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAAc                                                                                                     <  1:1069999/65‑1 (MQ=17)
                                                                                                                                     tgacccTGTCGCCGGCAAGCCAGCGACAGGGCCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAAc                                                                                                     >  2:1069999/4‑68 (MQ=17)
                                                                                                                                     tgacccTGTCGCCGGCAAGCCAGCGACAGGGCCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTg                   >  1:947896/4‑150 (MQ=255)
                                                                                                                                       gCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTGcc                 >  1:1139270/1‑150 (MQ=255)
                                                                                                                                        cccTGTCGCCGGCAAGCCAGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTg                                                              >  2:1106737/1‑104 (MQ=38)
                                                                                                                                        cccTGTCGCCGGCAAGCCAGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTg                                                              <  1:1106737/104‑1 (MQ=38)
                                                                                                                                         ccTGTCGCCGGCAAGCCAGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAgc                          <  1:854126/139‑1 (MQ=255)
                                                                                                                                         ccTGTCGCCGGCAAGCCAGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAgc                          >  2:854126/1‑139 (MQ=255)
                                                                                                                                          cTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTGCCGaa              <  2:1139270/150‑1 (MQ=255)
                                                                                                                                              cGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTGCCGAACCGa          <  1:1345106/150‑1 (MQ=255)
                                                                                                                                              cGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTGCCGAACCGa          <  2:551645/150‑1 (MQ=255)
                                                                                                                                                 tGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCActtgct                                                    >  1:466363/1‑105 (MQ=255)
                                                                                                                                                 tGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCActtgct                                                    <  2:466363/105‑1 (MQ=255)
                                                                                                                                                      tGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTGCCGAACCGATTCTCGgc  <  2:1012427/150‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                                     
GCCCGACTGTATGCGATCGTGATCACGTTCAGAGGGGCCTTGCACTGTTGCCTGCACATTGTAATCCAGCCCCTGACAAAGGGCCGTGGGCAGCAATATCATAATGACATCAATG‑CGCGGTGCGCACCACTCTGGCCCTGTCGCTGGCTTGCCGGCGACAGGGTCAGTACAGGCGATGTCAGAGCACCCGCTTGATCAACGGCTCCAACCGGCTATAGCGCAACCGACGCAGAAACTTGCGCACTTGCTTGGGATGTTCGGCCTTCTCCCCCAGCGCCTCTGCCGAACCGATTCTCGGC  >  NC_002947/4161999‑4162297

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A