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
A14 F1 I1 R1	71	51.6	2219666	95.9%	2128659	118.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,772,200	G→A	pseudogene (867/900 nt)	yfjV ←	pseudogene, CP4‑57 prophage,Phage or Prophage Related, putative pump protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,772,200	0	G	A	100.0%	208.2 / NA	60	pseudogene (867/900 nt)	yfjV	pseudogene, CP4‑57 prophage,Phage or Prophage Related, putative pump protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (36/24); total (36/24)

TGTCGGTTCGTTGCCGTTGTTATGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGTTGCCAGACTGCCAATCGGGGT  >  NC_000913/2772065‑2772331

tGTCGGTTCGTTGCCGTTGTTATGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGcc                                                                                                                                  >  1:354349/1‑139 (MQ=255)

  tCGGTTCGTTGCCGTTGTTATGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCag                                                                                                                                >  2:153291/1‑139 (MQ=255)

         gTTGCCGTTGTTATGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACa                                                                                                                         >  1:255517/1‑139 (MQ=255)

                     aTGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGc                                                                                                             <  2:372376/139‑1 (MQ=255)

                     aTGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGc                                                                                                             <  1:82765/139‑1 (MQ=255)

                     aTGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGc                                                                                                             <  2:355640/139‑1 (MQ=255)

                     aTGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGc                                                                                                             <  2:692191/139‑1 (MQ=255)

                     aTGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGc                                                                                                             <  1:1038923/139‑1 (MQ=255)

                      tGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGca                                                                                                            <  2:488788/139‑1 (MQ=255)

                      tGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGca                                                                                                            <  1:687664/139‑1 (MQ=255)

                       gAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGcac                                                                                                           <  1:271915/139‑1 (MQ=255)

                             tctcCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCAt                                                                                                     >  1:125066/1‑139 (MQ=255)

                             tctcCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCAt                                                                                                     >  1:1006056/1‑139 (MQ=255)

                               tcCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGa                                                                                                   >  2:364650/1‑139 (MQ=255)

                                     gtgtTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGc                                                                                             >  2:749982/1‑139 (MQ=255)

                                        ttGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCgg                                                                                          <  1:749982/139‑1 (MQ=255)

                                           cGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTAc                                                                                       <  2:296860/139‑1 (MQ=255)

                                             tGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACgg                                                                                     >  1:502390/1‑139 (MQ=255)

                                             tGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACgg                                                                                     >  2:1064206/1‑139 (MQ=255)

                                                  tGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTa                                                                                <  1:1064206/139‑1 (MQ=255)

                                                    ccACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAat                                                                              <  1:639808/139‑1 (MQ=255)

                                                                         aTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCatat                                                         >  2:272000/1‑139 (MQ=255)

                                                                            gTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAtttt                                                      >  2:60256/1‑139 (MQ=255)

                                                                             tAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGcac                                                                                                           >  2:956015/1‑85 (MQ=255)

                                                                             tAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGcac                                                                                                           <  1:956015/85‑1 (MQ=255)

                                                                             tAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAttttt                                                     >  2:624224/1‑139 (MQ=255)

                                                                                  ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTggg                                                <  2:1006056/139‑1 (MQ=255)

                                                                                    gCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCa                                              >  1:333865/1‑139 (MQ=255)

                                                                                    gCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCa                                              >  2:1027690/1‑139 (MQ=255)

                                                                                     cTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCACGTGATTGTCATATTTTTCAGGGCaa                                             >  2:471655/1‑139 (MQ=255)

                                                                                      tCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAg                                            <  2:396025/139‑1 (MQ=255)

                                                                                          atCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGcaca                                        >  2:1052845/1‑139 (MQ=255)

                                                                                          atCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGcaca                                        >  2:390947/1‑139 (MQ=255)

                                                                                               tATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAg                                            >  1:880545/1‑130 (MQ=255)

                                                                                               tATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAg                                            <  2:880545/130‑1 (MQ=255)

                                                                                                 tCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGcc                                 >  2:724600/1‑139 (MQ=255)

                                                                                                    aaTTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATcccc                                                                        <  2:572582/97‑1 (MQ=255)

                                                                                                    aaTTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATcccc                                                                        >  1:572582/1‑97 (MQ=255)

                                                                                                    aaTTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCcaca                              >  1:190766/1‑139 (MQ=255)

                                                                                                    aaTTACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCcaca                              >  2:578315/1‑139 (MQ=255)

                                                                                                       tACAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCAcagca                           >  1:897880/1‑139 (MQ=255)

                                                                                                        aCAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCAcagcag                          <  2:125066/139‑1 (MQ=255)

                                                                                                        aCAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCAcagcag                          <  1:724600/139‑1 (MQ=255)

                                                                                                         cAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGca                                                                                                            >  1:687206/1‑56 (MQ=255)

                                                                                                         cAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGca                                                                                                            <  2:687206/56‑1 (MQ=255)

                                                                                                         cAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCaga                         >  1:430164/1‑139 (MQ=255)

                                                                                                         cAAAGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCaga                         >  2:75725/1‑139 (MQ=255)

                                                                                                            aGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTa                                                                                        >  1:158328/1‑73 (MQ=255)

                                                                                                            aGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTa                                                                                        <  2:158328/73‑1 (MQ=255)

                                                                                                            aGTGACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGtt                      >  1:930577/1‑139 (MQ=255)

                                                                                                               gACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGca                                                                                                            <  1:515256/50‑1 (MQ=255)

                                                                                                               gACAGAGAGCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGca                                                                                                            >  2:515256/1‑50 (MQ=255)

                                                                                                                  agagagCCGCCACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGTTGCCAGa                <  1:495389/139‑1 (MQ=255)

                                                                                                                        ccgccACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAata                                                                             <  1:1106970/72‑1 (MQ=255)

                                                                                                                        ccgccACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAata                                                                             >  2:1106970/1‑72 (MQ=255)

                                                                                                                        ccgccACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGTTGCCAGACTGCCa          >  1:503162/1‑139 (MQ=255)

                                                                                                                        ccgccACGCCAGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGTTGCCAGACTGCCa          >  2:840578/1‑139 (MQ=255)

                                                                                                                           ccacgccaGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGCTTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGTTGCCAGACTGCCAATc       >  1:349799/1‑139 (MQ=255)

                                                                                                                            cacgccaGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGTTGCCAGACTGCCAATCg      >  1:36807/1‑139 (MQ=255)

                                                                                                                                ccaGCGCAGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGTTGCCAGACTGCCAATCGGGGt  >  1:878980/1‑139 (MQ=255)

TGTCGGTTCGTTGCCGTTGTTATGAAGCATCTCCAGCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCACAGCAGAGTTGCCAGACTGCCAATCGGGGT  >  NC_000913/2772065‑2772331

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