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 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,426,288 G→A intergenic (+206/‑166) ydaY → / → tmpR pseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,426,2880GA100.0% 212.1 / NA 67intergenic (+206/‑166)ydaY/tmpRpseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/36);  total (31/36)

GGTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGC  >  NC_000913/1426156‑1426405
                                                                                                                                     |                                                                                                                     
ggTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                 >  2:640732/1‑139 (MQ=255)
  tgcctttgccttTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAAt                                                                                                               <  2:1488817/139‑1 (MQ=255)
     ctttgcctttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATAGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTTCAGGGGCAGTGTGTGTAATTGTTAATTa                                                                                                             >  2:1010648/1‑139 (MQ=255)
          cctttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       <  1:1251314/139‑1 (MQ=255)
          cctttATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       <  1:28661/139‑1 (MQ=255)
                  tctGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTa                                                                                               <  1:715279/139‑1 (MQ=255)
                          agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                 >  2:586342/1‑113 (MQ=255)
                          agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTa                                                                                                                 <  1:586342/113‑1 (MQ=255)
                          agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACa                                                                                             <  1:476991/133‑1 (MQ=255)
                          agaTAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACa                                                                                             >  2:476991/1‑133 (MQ=255)
                                 tGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGgt                                                                                <  2:566823/139‑1 (MQ=255)
                                  gAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGgtg                                                                               >  1:412279/1‑139 (MQ=255)
                                     tatTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCt                                                                            >  2:619582/1‑139 (MQ=255)
                                      atTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       <  2:1197772/111‑1 (MQ=255)
                                      atTTAGCCACTCATCCGGTATCGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       >  1:1197772/1‑111 (MQ=255)
                                          aGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat                                                                       >  2:421532/1‑139 (MQ=255)
                                                  aTCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACActc                                                                                                    >  1:993900/1‑102 (MQ=255)
                                                  aTCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACActc                                                                                                    <  2:993900/102‑1 (MQ=255)
                                                     cGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCgatga                                                            <  1:619582/139‑1 (MQ=255)
                                                           tgattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTcc                                                      <  2:803489/139‑1 (MQ=255)
                                                                gaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGgag                                                 >  1:382625/1‑139 (MQ=255)
                                                                 aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       <  1:643552/84‑1 (MQ=255)
                                                                 aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTaca                                                                                                       >  2:643552/1‑84 (MQ=255)
                                                                 aGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGgaga                                                <  1:640732/139‑1 (MQ=255)
                                                                  gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTaa                                                                                                                <  1:710035/74‑1 (MQ=255)
                                                                  gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTaa                                                                                                                >  2:710035/1‑74 (MQ=255)
                                                                  gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGaa                                               >  1:63220/1‑139 (MQ=255)
                                                                  gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGaa                                               >  2:1165304/1‑139 (MQ=255)
                                                                  gcgcGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGaa                                               >  1:322540/1‑139 (MQ=255)
                                                                       aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         <  2:1445136/76‑1 (MQ=255)
                                                                       aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         >  1:1445136/1‑76 (MQ=255)
                                                                       aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGAtgtg                                                                                     >  2:638570/1‑96 (MQ=255)
                                                                       aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGAtgtg                                                                                     <  1:638570/96‑1 (MQ=255)
                                                                                     gTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGt                            >  2:632684/1‑139 (MQ=255)
                                                                                      tGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         >  1:211656/1‑61 (MQ=255)
                                                                                      tGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         <  2:211656/61‑1 (MQ=255)
                                                                                      tGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTCAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTa                           >  1:914137/1‑139 (MQ=255)
                                                                                       gATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTaa                          <  2:382625/139‑1 (MQ=255)
                                                                                       gATCTTTGCACTCGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCCGGAGAAAAGCATTGCGTGGCCTCGTaa                          <  2:914137/139‑1 (MQ=255)
                                                                                          cTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCg                       <  2:63220/139‑1 (MQ=255)
                                                                                            ttGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     <  1:632684/139‑1 (MQ=255)
                                                                                            ttGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     <  2:274831/139‑1 (MQ=255)
                                                                                               cACTCGATGACCAGTATTTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCTTGGCCTCGTAATCGCtat                   <  1:1010648/139‑1 (MQ=255)
                                                                                                 cTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATc                <  1:421532/139‑1 (MQ=255)
                                                                                                    gATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     >  1:200684/1‑131 (MQ=255)
                                                                                                    gATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     <  2:200684/131‑1 (MQ=255)
                                                                                                    gATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATctac             >  1:729042/1‑139 (MQ=255)
                                                                                                         ccAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAAt                                                                  <  1:104024/81‑1 (MQ=255)
                                                                                                         ccAGTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAAt                                                                  >  2:104024/1‑81 (MQ=255)
                                                                                                            gTA‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGt     <  1:1165304/139‑1 (MQ=255)
                                                                                                              a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         >  2:1348862/1‑37 (MQ=255)
                                                                                                              a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTa                                                                                                         <  1:1348862/37‑1 (MQ=255)
                                                                                                              a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat                                                                       >  2:743761/1‑71 (MQ=255)
                                                                                                              a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat                                                                       <  1:743761/71‑1 (MQ=255)
                                                                                                              a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCg                                     >  2:1386112/1‑105 (MQ=255)
                                                                                                              a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCg                                     <  1:1386112/105‑1 (MQ=255)
                                                                                                              a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCtat                   >  1:1069362/1‑123 (MQ=255)
                                                                                                              a‑TTTTCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCtat                   <  2:1069362/123‑1 (MQ=255)
                                                                                                                ttttCAGGAGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGc  <  2:729042/139‑1 (MQ=255)
                                                                                                                        aGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTc                                                                             >  1:897683/1‑56 (MQ=255)
                                                                                                                        aGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTc                                                                             <  2:897683/56‑1 (MQ=255)
                                                                                                                        aGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTg                                                    >  1:173520/1‑81 (MQ=255)
                                                                                                                        aGCAGTGTGTGTAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTg                                                    <  2:173520/81‑1 (MQ=255)
                                                                                                                             tgtgtgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTa                           >  2:72261/1‑101 (MQ=255)
                                                                                                                             tgtgtgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTa                           <  1:72261/101‑1 (MQ=255)
                                                                                                                                 tgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     <  2:724689/103‑1 (MQ=255)
                                                                                                                                 tgtAATTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCt                     >  1:724689/1‑103 (MQ=255)
                                                                                                                                     |                                                                                                                     
GGTGCCTTTGCCTTTATCTCTGACAGAGATAAATGAATATTTAGCCACTCATCCGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTA‑TTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGATGATGCTCCTGGAGAAAAGCATTGCGTGGCCTCGTAATCGCTATATCTACTATTATGTCGC  >  NC_000913/1426156‑1426405

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