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	128	54.7	1845674	99.3%	1832754	139.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,769,648	(C)_6→7	intergenic (+162/‑55)	yfjQ → / → yfjR	CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,769,642	1	.	C	100.0%	180.6 / NA	49	intergenic (+156/‑61)	yfjQ/yfjR	CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (26/23); total (26/23)

TTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGG  >  NC_000913/2769508‑2769776

ttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑c                                                                                                                                   <  1:240037/140‑1 (MQ=255)

ttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑c                                                                                                                                   >  1:499155/1‑140 (MQ=255)

 tAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑cc                                                                                                                                  <  2:383150/140‑1 (MQ=255)

 tAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑cc                                                                                                                                  <  1:447368/140‑1 (MQ=255)

 tAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑cc                                                                                                                                  <  1:459099/140‑1 (MQ=255)

        ggACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTa                                                                                                                            <  1:34652/140‑1 (MQ=255)

          acacCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTaaa                                                                                                                          >  1:399906/1‑140 (MQ=255)

          acacCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGGTTCTCCGTTGTCCATACCCTGTCCG‑CCCCACCCCTTTaaa                                                                                                                          >  2:591686/1‑140 (MQ=38)

            accaccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGt                                                                                                                        >  1:590303/1‑140 (MQ=255)

              caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTaa                                                                                                                      >  2:667465/1‑140 (MQ=255)

              caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTaa                                                                                                                      >  2:472180/1‑140 (MQ=255)

              caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTaa                                                                                                                      >  1:686789/1‑140 (MQ=255)

              caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑ccctct                                                                                                                              <  2:94706/131‑5 (MQ=255)

              caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑ccctct                                                                                                                              >  1:94706/1‑127 (MQ=255)

                  tGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATcac                                                                                                                  <  2:499155/140‑1 (MQ=255)

                   gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATcaca                                                                                                                 >  2:252340/1‑140 (MQ=255)

                   gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATcaca                                                                                                                 <  1:608411/140‑1 (MQ=255)

                   gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATcaca                                                                                                                 >  1:274998/1‑140 (MQ=255)

                        cATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCAtt                                                                                                            >  1:901148/1‑140 (MQ=255)

                        cATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCAtt                                                                                                            <  2:590303/140‑1 (MQ=255)

                           cGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTtc                                                                                                         <  2:179162/140‑1 (MQ=255)

                               aTGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTtcagtc                                                                                                     <  1:640922/140‑1 (MQ=255)

                               aTGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTtcagtc                                                                                                     <  2:840718/140‑1 (MQ=255)

                                   gCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                 <  2:399906/140‑1 (MQ=255)

                                          tgCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTc                                                                                          <  1:785950/140‑1 (MQ=255)

                                            ccTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCt                                                                                        >  2:868574/1‑140 (MQ=255)

                                            ccTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCt                                                                                        >  1:111805/1‑140 (MQ=255)

                                                aaTCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGgag                                                                                    <  1:667465/140‑1 (MQ=255)

                                                  tCCCCCGGTTATAGCTTTTAACCCCCGTTATATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGaa                                                                                  <  1:746482/140‑1 (MQ=255)

                                                    ccccGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtc                                                                                <  2:686789/140‑1 (MQ=255)

                                                       cGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctct                                                                             >  1:549933/1‑140 (MQ=255)

                                                       cGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctct                                                                             >  1:317131/1‑140 (MQ=255)

                                                              aGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGaca                                                                      >  2:361320/1‑140 (MQ=255)

                                                               gCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGacac                                                                     <  1:472180/140‑1 (MQ=255)

                                                                          ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGac                                                                       <  1:672693/127‑1 (MQ=255)

                                                                          ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGac                                                                       >  2:672693/1‑127 (MQ=255)

                                                                                     ggCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCg                                               >  1:839999/1‑140 (MQ=255)

                                                                                      gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCgg                                              >  2:255803/1‑140 (MQ=255)

                                                                                      gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCgg                                              >  2:858174/1‑140 (MQ=255)

                                                                                      gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTAATGACACAGGCAGAACGCCGCCATGACCgg                                              >  2:564717/1‑140 (MQ=255)

                                                                                       cTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggc                                             >  2:330535/1‑140 (MQ=255)

                                                                                              aGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgt                                      <  2:901148/140‑1 (MQ=255)

                                                                                                      aaaaTAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtcaggctgt                              <  1:330535/140‑1 (MQ=255)

                                                                                                         aTAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCAc                           <  2:549933/140‑1 (MQ=255)

                                                                                                           aGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTg                         <  1:361320/140‑1 (MQ=255)

                                                                                                            gTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGa                        >  2:740657/1‑140 (MQ=255)

                                                                                                             tttCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGAt                       <  1:740657/140‑1 (MQ=255)

                                                                                                             tttCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGAt                       <  1:69500/140‑1 (MQ=255)

                                                                                                                   cGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAg                 <  2:317131/140‑1 (MQ=255)

                                                                                                                       gTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGt             <  2:274998/140‑1 (MQ=255)

                                                                                                                              cccTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTg      <  1:252340/140‑1 (MQ=255)

                                                                                                                                  gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:676346/1‑140 (MQ=255)

                                                                                                                                  gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:702368/1‑140 (MQ=255)

                                                                                                                                  gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:900122/1‑140 (MQ=255)

                                                                                                                                  gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:396209/1‑140 (MQ=255)

                                                                                                                                  gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:131631/1‑140 (MQ=255)

                                                                                                                                  gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:393496/1‑140 (MQ=255)

                                                                                                                                  gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:595650/1‑140 (MQ=255)

TTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGG  >  NC_000913/2769508‑2769776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A