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 F28 I1 R1	164	66.7	2276140	99.1%	2255654	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,767,507	(C)_7→9	intergenic (+152/‑203)	rnlB → / → yfjP	CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,767,500	1	.	C	100.0%	162.4 / NA	45	intergenic (+145/‑210)	rnlB/yfjP	CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (21/24); total (21/24)
*	NC_000913	2,767,500	2	.	C	100.0%	165.5 / NA	45	intergenic (+145/‑210)	rnlB/yfjP	CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (21/24); total (21/24)

TCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑‑CCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCAGATAGA  >  NC_000913/2767366‑2767629

||

tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑‑ccc‑cc                                                                                                                               <  1:200832/140‑1 (MQ=255)

 ctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑‑ccc‑ccc                                                                                                                              <  1:1010725/140‑1 (MQ=255)

             gTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACtt                                                                                                                   <  1:442349/140‑1 (MQ=255)

                                ggCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAAtt                                                                                                <  2:1027499/140‑1 (MQ=255)

                                      atatTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTgg                                                                                          <  1:112577/140‑1 (MQ=255)

                                      atatTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTgg                                                                                          <  2:1051574/140‑1 (MQ=255)

                                         ttAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGaaa                                                                                       <  2:598726/140‑1 (MQ=255)

                                                 tCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatga                                                                               >  2:515353/1‑140 (MQ=255)

                                                  ccAATATGATCAAATAGCATTAACCCCCCCTCACAACGTACTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTCATTTT‑‑CCCACCCCATTTAAAATTCTCAATAATGTCAACACTTTTCCGGAAATCCTattac                                                                              >  2:138129/1‑137 (MQ=255)

                                                   cAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatgatg                                                                             >  2:249194/1‑140 (MQ=255)

                                                      tatGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGcc                                                                           <  1:632066/139‑1 (MQ=255)

                                                      tatGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGcc                                                                           >  2:632066/1‑139 (MQ=255)

                                                        ttaTCAAATAGCATTCACCCCCCCCCACAACGTTCTTGATAGGGAACACGTTTTCCCCTATGCACCCCCGACTGAATTTCCCCC‑CCCC‑CTTAAACTTCTCAAGAATGTCACCAATTTTCTGGAAATCCTATGATGCCttt                                                                        <  2:419801/138‑1 (MQ=255)

                                                           tCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTccc                                                                     <  2:868996/140‑1 (MQ=255)

                                                            cAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg                                                                    >  1:557042/1‑140 (MQ=255)

                                                                tAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa                                                                >  2:758083/1‑140 (MQ=255)

                                                                 aGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaaa                                                               <  1:950975/140‑1 (MQ=255)

                                                                    aTTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTCCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAACCTTCTCAATAATGTCACCAATTTTCTATTACTCCTATTATGCGTTTCCCGGTAAAttt                                                            >  2:669483/1‑138 (MQ=255)

                                                                    aTTAA‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGt                                                           >  1:780096/1‑140 (MQ=255)

                                                                     ttAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGt                                                           >  2:776752/1‑140 (MQ=255)

                                                                     ttAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGt                                                           >  1:644451/1‑140 (MQ=255)

                                                                        aCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCt                                                        <  1:387342/140‑1 (MQ=255)

                                                                             cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCTCGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa                                                                <  2:948741/127‑1 (MQ=255)

                                                                             cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg                                                                    >  2:979241/1‑123 (MQ=255)

                                                                             cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg                                                                    <  1:979241/123‑1 (MQ=255)

                                                                             cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa                                                                >  1:948741/1‑127 (MQ=255)

                                                                             cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAg                                                   <  1:669483/140‑1 (MQ=255)

                                                                                         ccTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGAtt                                       >  2:457895/1‑140 (MQ=255)

                                                                                         ccTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGAtt                                       >  2:441379/1‑140 (MQ=255)

                                                                                          cTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTc                                      >  2:930310/1‑140 (MQ=255)

                                                                                           tGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCt                                     <  1:441379/140‑1 (MQ=255)

                                                                                            gCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTg                                    <  1:254588/140‑1 (MQ=255)

                                                                                            gCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTg                                    <  1:138129/140‑1 (MQ=255)

                                                                                            gCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTg                                    <  1:831590/140‑1 (MQ=255)

                                                                                             cATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGc                                   <  1:999700/140‑1 (MQ=255)

                                                                                               tAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCaa                                 <  2:844648/140‑1 (MQ=255)

                                                                                               tAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCaa                                 <  2:780096/140‑1 (MQ=255)

                                                                                                  ggAACACGTTTTCTCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCt                              >  2:706762/1‑140 (MQ=255)

                                                                                                  ggAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATc                               >  2:242356/1‑139 (MQ=255)

                                                                                                  ggAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATc                               <  1:242356/139‑1 (MQ=255)

                                                                                                  ggAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCt                              >  2:801949/1‑140 (MQ=255)

                                                                                                       acGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTAtgtg                         >  2:270643/1‑140 (MQ=255)

                                                                                                       acGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTAtgtg                         >  1:946186/1‑140 (MQ=255)

                                                                                                               cccGGTGCACCCACGAGTAAATTTCCCCC‑CCCC‑TGTAAACTTCTCAATAATGTCGCCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTGCAGAAAGATTCTGCAATCTAAGTGCATTGaaa                 <  2:399395/140‑1 (MQ=255)

                                                                                                                ccTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGaaaa                <  2:644451/140‑1 (MQ=255)

                                                                                                                   gtgCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAAt             >  1:182133/1‑140 (MQ=255)

                                                                                                                      cACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCtt          <  1:706762/140‑1 (MQ=255)

                                                                                                                         ccACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCCATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCag       >  1:970873/1‑140 (MQ=255)

                                                                                                                          cACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCaga      <  1:475340/140‑1 (MQ=255)

                                                                                                                           aCGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCagat     <  1:515353/140‑1 (MQ=255)

                                                                                                                           aCGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCagat     <  2:616311/140‑1 (MQ=255)

                                                                                                                            cGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCag       >  2:642058/1‑137 (MQ=255)

                                                                                                                            cGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCag       <  1:642058/137‑1 (MQ=255)

                                                                                                                              aCTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCagataga  >  1:474947/1‑140 (MQ=255)

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TCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑‑CCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCAGATAGA  >  NC_000913/2767366‑2767629

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A