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
A4 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,863 C→T pseudogene (19/48 nt) rph ← ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,8630CT100.0% 190.5 / NA 59pseudogene (19/48 nt)rphribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/29);  total (30/29)

AGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGT  >  NC_000913/3815731‑3815993
                                                                                                                                    |                                                                                                                                  
aGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAAt                                                                                                                              >  1:152929/1‑139 (MQ=255)
  cgcAAATTCAATAAATTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATgg                                                                                                                            >  1:1118636/1‑139 (MQ=255)
  cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATgg                                                                                                                            >  1:1106723/1‑139 (MQ=255)
  cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATgg                                                                                                                            >  1:1264888/1‑139 (MQ=255)
       aTTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcg                                                                                                                       >  1:126570/1‑139 (MQ=255)
          cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                    <  2:1264888/139‑1 (MQ=255)
          cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                    <  1:60485/139‑1 (MQ=255)
                     cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGcc                                                                                                         >  1:1037084/1‑139 (MQ=255)
                            atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGTCAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTACTGCGACGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCca                                                                                                  <  2:1118636/139‑1 (MQ=255)
                                  tCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGa                                                                                            >  1:1063739/1‑139 (MQ=255)
                                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAGAAAAAGGCGGATCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTACTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCag                                                                                                       >  2:1062035/1‑126 (MQ=255)
                                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                    <  2:772473/113‑1 (MQ=255)
                                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                    >  1:772473/1‑113 (MQ=255)
                                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCag                                                                                                       <  1:1062035/126‑1 (MQ=255)
                                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAg                                                                                             >  2:985819/1‑136 (MQ=255)
                                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAg                                                                                             <  1:985819/136‑1 (MQ=255)
                                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                          >  2:1571983/1‑139 (MQ=255)
                                         ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                     <  1:1571983/139‑1 (MQ=255)
                                            gCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                          <  2:1291459/131‑1 (MQ=255)
                                            gCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                          >  1:1291459/1‑131 (MQ=255)
                                              tcctcATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTGAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                <  2:1106723/139‑1 (MQ=255)
                                                  cATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                                          >  2:748744/1‑109 (MQ=255)
                                                  cATCTTACTTTTCTACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                                          <  1:748744/109‑1 (MQ=255)
                                                               tACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                    >  1:1135643/1‑86 (MQ=255)
                                                               tACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                    <  2:1135643/86‑1 (MQ=255)
                                                               tACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                                          <  2:742627/96‑1 (MQ=255)
                                                               tACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                                          >  1:742627/1‑96 (MQ=255)
                                                               tACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCa                                                                                                        >  1:1240316/1‑98 (MQ=255)
                                                               tACAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCa                                                                                                        <  2:1240316/98‑1 (MQ=255)
                                                                 cAGACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                             <  2:1037084/139‑1 (MQ=255)
                                                                   gACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                    >  2:162546/1‑82 (MQ=255)
                                                                   gACAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                                    <  1:162546/82‑1 (MQ=255)
                                                                    aCAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                          >  1:855652/1‑107 (MQ=255)
                                                                    aCAAAAAAAAGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                                                                          <  2:855652/107‑1 (MQ=255)
                                                                      aaaaaaaaGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCa                                                                                                        >  1:1213997/1‑91 (MQ=255)
                                                                      aaaaaaaaGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCa                                                                                                        <  2:1213997/91‑1 (MQ=255)
                                                                      aaaaaaaaGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                        >  2:1164796/1‑139 (MQ=255)
                                                                             aGGCGGCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                 <  2:1063739/139‑1 (MQ=255)
                                                                              ggcggcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                <  2:152929/139‑1 (MQ=255)
                                                                                cggcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGATTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                              >  2:92881/4‑139 (MQ=255)
                                                                                cggcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                     >  2:904687/4‑100 (MQ=255)
                                                                                cggcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                     <  1:904687/97‑1 (MQ=255)
                                                                                cggcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                              <  2:1459048/136‑1 (MQ=255)
                                                                                  gcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGcc                                                                                                   >  2:1175042/2‑84 (MQ=255)
                                                                                  gcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGcc                                                                                                   <  1:1175042/83‑1 (MQ=255)
                                                                                  gcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                >  2:686537/2‑103 (MQ=255)
                                                                                  gcTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                <  1:686537/102‑1 (MQ=255)
                                                                                   cTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                             <  2:1245336/121‑1 (MQ=255)
                                                                                   cTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                             >  1:1245336/1‑121 (MQ=255)
                                                                                           tCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                      >  1:355714/1‑120 (MQ=255)
                                                                                           tCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                      <  2:355714/120‑1 (MQ=255)
                                                                                             gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                 >  1:1354138/1‑139 (MQ=255)
                                                                                               cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcg                               <  1:1164796/139‑1 (MQ=255)
                                                                                                          gTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg                    <  2:126570/139‑1 (MQ=255)
                                                                                                           tttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                   >  1:642635/1‑139 (MQ=255)
                                                                                                                cAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca              <  2:642635/139‑1 (MQ=255)
                                                                                                                   cgccgcCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTa           <  2:1354138/139‑1 (MQ=255)
                                                                                                                            cTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGt  >  1:206057/1‑139 (MQ=255)
                                                                                                                            cTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGt  >  1:1221883/1‑139 (MQ=255)
                                                                                                                                    |                                                                                                                                  
AGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGT  >  NC_000913/3815731‑3815993

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A