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
A2 F28 I1 R1	155	60.3	2039550	99.3%	2025273	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,071,643	T→C	G35G (GGT→GGC)	flu →	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,071,643	0	T	C	100.0%	149.0 / NA	42	G35G (GGT→GGC)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (21/21); total (21/21)

TTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGATTGTCTTCGGTACGACC  >  NC_000913/2071507‑2071778

tttttATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACgtggcggcgtg                                                                                                                                      >  1:915781/1‑140 (MQ=255)

tttttATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACgtggcggcgta                                                                                                                                      >  1:564695/1‑139 (MQ=255)

    tATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAAcgtggcggcgtggcgg                                                                                                                                  <  1:701501/140‑1 (MQ=255)

    tATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAAcgtggcggcgtggcgg                                                                                                                                  <  2:252058/140‑1 (MQ=255)

     aTTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACgtggcggcgtggcggt                                                                                                                                 <  1:650497/140‑1 (MQ=255)

     aTTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACgtggcggcgtggcggt                                                                                                                                 <  2:382319/140‑1 (MQ=255)

             tCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGt                                                                                                                         >  2:959599/1‑140 (MQ=255)

                aTCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGtctc                                                                                                                      >  1:1004114/1‑140 (MQ=255)

                     aGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTctct                                                                                                                     <  1:555309/136‑1 (MQ=255)

                     aGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTctct                                                                                                                     >  2:555309/1‑136 (MQ=255)

                     aGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGGTGTACTGTCTCTTTcc                                                                                                                 >  2:758868/1‑140 (MQ=255)

                     aGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGCAAACGTGGCGGCGTGGCGGGTGCCCTATCTTTTTcc                                                                                                                 >  1:791995/1‑140 (MQ=255)

                      ggAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCg                                                                                                                <  2:466045/140‑1 (MQ=255)

                        aaaaGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCa                                                                                                              <  1:758868/140‑1 (MQ=255)

                         aaaGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAg                                                                                                             <  1:178886/140‑1 (MQ=255)

                          aaGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAgt                                                                                                            <  2:1004114/140‑1 (MQ=255)

                           aGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGGACCGTCTCTTTCCGccggc                                                                                                           >  2:330496/1‑136 (MQ=255)

                           aGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTTCCGccggc                                                                                                           >  2:184441/1‑136 (MQ=255)

                           aGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTTCCGCCgtc                                                                                                           >  1:106399/1‑140 (MQ=255)

                           aGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAgtc                                                                                                           >  1:794103/1‑140 (MQ=255)

                              tgatgaAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAgtcacg                                                                                                        <  1:984051/140‑1 (MQ=255)

                                atgaAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTTCCCCCgtcacgtc                                                                                                      >  2:563797/1‑140 (MQ=255)

                                                      gCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCCCATTCTCCTTTCGCCCTCACGTCCCCCCCCGGGCCGGCTGCTCAc                                                                                >  1:200007/1‑140 (MQ=255)

                                                       cTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCCCTGTCTCTTGCCGCCGTCACGTCCCTCCCCGGGCCGGCTGCTGACa                                                                               >  2:439386/1‑140 (MQ=255)

                                                       cTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTACACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACa                                                                               >  1:332534/1‑140 (MQ=255)

                                                       cTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGGTGCACTGTCTCTTTCCGCCGGCACGTCCCTCCCCGGGGCGGCTGCTGGCa                                                                               >  2:394463/1‑140 (MQ=255)

                                                               tGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTTCACCGTCTCTTTCCGCAGGCACCGCACTCCCCGTGCTTGCCGCTGACCTCGTtgtg                                                                       >  1:232482/1‑140 (MQ=255)

                                                               tGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACCTCCCTCCCCGTGCTGGCTGCTGACATCGTtgtg                                                                       >  1:396932/1‑140 (MQ=255)

                                                                            caTGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTTCCCCAGTCACGGCACTCCCCGGGCTGGCTGCTGACAACGTTGTGCACCCCGGGGaaa                                                          >  2:38911/1‑140 (MQ=255)

                                                                            caTGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCCGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGaaa                                                          >  1:808541/1‑140 (MQ=255)

                                                                             aTGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTTCCGCCGGCACGTCACTCCCCGGGCCGGCTGCTGACATCGTTTTGCACCCCGGGGaaaa                                                         >  2:334910/1‑139 (MQ=255)

                                                                                 cGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCCCTCCCGGGGCTGGCTGCTGACATCGTTGTGCACCCGGGGGGAACCGTg                                                     >  2:363487/1‑140 (MQ=255)

                                                                                 cGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTg                                                     <  2:794103/140‑1 (MQ=255)

                                                                                   ggCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGaa                                                   <  1:184441/140‑1 (MQ=255)

                                                                                     cgcTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAAcg                                                 <  2:915781/140‑1 (MQ=255)

                                                                                     cgcTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTAGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAAcg                                                 <  2:564695/140‑1 (MQ=255)

                                                                                         ttCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCCGTCACGTCACTCCCCGTGCTGGCCGCTGCCAACGTTGTGCACCCCGGGGAAACCGTGGAcggcgg                                             >  2:965628/1‑140 (MQ=255)

                                                                                           cGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGaa                                           <  1:563797/140‑1 (MQ=255)

                                                                                                     tCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCaaa                                 <  1:959599/140‑1 (MQ=255)

                                                                                                         aaCTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCAt                             <  1:334910/140‑1 (MQ=255)

                                                                                                         aaCTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCAt                             <  1:643763/140‑1 (MQ=255)

                                                                                                           cTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGa                           <  1:770231/140‑1 (MQ=255)

                                                                                                             ggCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTACACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACa                         <  2:332534/140‑1 (MQ=255)

                                                                                                              gCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACaa                        <  1:996869/140‑1 (MQ=255)

                                                                                                                   cgcACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGa                   <  1:363487/140‑1 (MQ=255)

                                                                                                                    gacaggggTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGAt                  <  1:998105/136‑1 (MQ=255)

                                                                                                                     cACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGAtt                 <  1:38911/140‑1 (MQ=255)

                                                                                                                     cACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGAtt                 <  2:429083/140‑1 (MQ=255)

                                                                                                                                 gtggcggcgtggcggtTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGATTGTCTTCGGTACg     <  2:232482/140‑1 (MQ=255)

                                                                                                                                 gtggcggcgtggcggtTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGATTGTCTTCGGTACg     <  2:396932/140‑1 (MQ=255)

                                                                                                                                  tggcggcgtggcggtTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCCGGGCTGGCTGCTGACATCGTTGTGCACCCGGGGGAAACCGTGAACGGCGGGACACTGGCAAAACATTACAAACAGATTGTCTTCGGTACGa    >  2:817035/1‑140 (MQ=255)

                                                                                                                                    gcggcgtggcggtTGCACTGTCTCTTGCCGCCGTCACGTCACTCCCCGGGCTGGGTGCTGACATCGTTGTGCACCCGGGGGGAAACGTGAACGGCGGGACACTGGCAAAACATGACAACCAGATTGTCTTCGGGACGAcc  >  2:388708/1‑140 (MQ=255)

                                                                                                                                    gcggcgtggcggtTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGGGCTGGCTGCTGACATCGTTGTGCACCCCGGGGAAAACGTGAACGGGGGGACACCGGCAAAACATGACAAACAGATTGTTTTTGGTActgtc  >  2:998105/1‑136 (MQ=255)

                                                                                                                                    gcggcgtggcggtTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCCGGGCTGGCTGCTGACATCGTTGTGCACCCGGGGGAAACCGTGAACGGCGGGACACTGGCAAAACATGACAACCAGATTGTCTTCGGTGCGAcc  >  2:334477/1‑140 (MQ=255)

                                                                                                                                    gcggcgtggcggtTGCACTGTCTCTTGCCGCAGTCACCTCACCCCCGGTGCTGGCTGCTGACATCGTTTTGCACCCCGGGGAAAACGTGAACGGCGGGACACTGGCAAAACATGACAACCAGAATGTCTTCGGGACGAcc  >  2:602300/1‑140 (MQ=255)

TTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGATTGTCTTCGGTACGACC  >  NC_000913/2071507‑2071778

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