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
A13 F63 I0 R1	31	53.1	1128482	96.8%	1092370	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,856,087	T→A	100%	P80P (CCT→CCA)	USA300HOU_2698 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,856,087	0	T	A	100.0%	168.7 / ‑6.5	53	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); major base A (26/26); minor base G (0/1); total (26/27)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGAGATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTC  >  CP000730/2855949‑2856223

ggAGATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGCTGTGTCATGCAATCATGCGCCaaa                                                                                                                                        >  2:118922/1‑141 (MQ=255)

 gagaTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGATATGTGTCATGCAATCATGCGCCaaaa                                                                                                                                       >  1:343399/1‑141 (MQ=255)

   gaTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACg                                                                                                                                     >  2:552568/1‑141 (MQ=255)

     tGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTc                                                                                                                                   >  2:389499/1‑141 (MQ=255)

     tGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTc                                                                                                                                   >  2:81781/1‑141 (MQ=255)

       cATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTGCAGCACCAACTACAGTTTAAAAGGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGAGCCAAAACGTcaa                                                                                                                                 >  1:150235/1‑141 (MQ=255)

        ctGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaac                                                                                                                                <  2:195355/140‑1 (MQ=255)

         tGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaaca                                                                                                                               <  1:347907/141‑1 (MQ=255)

                                 caaatTCGAACAAGCTTTAGTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATTGTTTTTATAGTTGTTAc                                                                                                       <  1:248527/138‑1 (MQ=255)

                                   tatTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcag                                                                                                     <  2:210766/141‑1 (MQ=255)

                                   aatTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcag                                                                                                     <  2:96304/140‑1 (MQ=255)

                                    atTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagc                                                                                                    <  1:55694/141‑1 (MQ=255)

                                    atTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagc                                                                                                    <  1:540767/141‑1 (MQ=255)

                                     ttGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagca                                                                                                   >  1:391360/1‑141 (MQ=255)

                                        gAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAGTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAgcagca                                                                                                >  2:90395/1‑141 (MQ=255)

                                        gAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAgcagca                                                                                                >  2:91723/1‑141 (MQ=255)

                                         aaCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCAt                                                                                               >  1:179424/1‑141 (MQ=255)

                                         aaCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCAt                                                                                               <  2:109997/141‑1 (MQ=255)

                                            aaGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAg                                                                                            <  2:224161/141‑1 (MQ=255)

                                                tttAGTTCAGCACCAACTCCATTTTAAAACAGAAGTTCAGTCATCATTACCTTGTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCACAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGatag                                                                                        >  2:341644/1‑140 (MQ=255)

                                                  tATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTg                                                                                      <  1:12536/141‑1 (MQ=255)

                                                             cAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGt                                                                           <  1:552568/141‑1 (MQ=255)

                                                             cAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGt                                                                           >  1:348730/1‑141 (MQ=255)

                                                             cAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGGGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACgg                                                                           >  1:23803/1‑140 (MQ=255)

                                                                 tACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCAc                                                                       <  1:317263/141‑1 (MQ=255)

                                                                  aCATTTTAAAACAGAAATGCAATCAACATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACTTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACt                                                                      <  1:114204/141‑1 (MQ=255)

                                                                      tttAAAACGGAAGTGCAGTCATCATTACCTTTTAAGGTAACAGGAGATGTGTCATGTAATCATGCGCCAAAACGTCAACAAATGCTAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGtt                                                                  <  2:179617/141‑1 (MQ=255)

                                                                       ttAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTa                                                                 >  2:556218/1‑141 (MQ=255)

                                                                              ggAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGa                                                          <  2:525424/141‑1 (MQ=255)

                                                                              ggAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGa                                                          >  2:281113/1‑141 (MQ=255)

                                                                               gAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGaa                                                         <  2:179424/141‑1 (MQ=255)

                                                                                  gTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTGATAGTTGTTACAGCAGCAGTAGATATTGAATTATTACGTTCACTGGTTCCAACAGAattt                                                      >  2:86856/1‑141 (MQ=255)

                                                                                       gTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTg                                                 >  2:216989/1‑141 (MQ=255)

                                                                                       gTCATCATTACCATTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTCTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTAACTGGTTACACAAGAatttcttta                                                 >  2:14075/1‑140 (MQ=255)

                                                                                        tcatcaTTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCGAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTgg                                                <  2:478468/141‑1 (MQ=255)

                                                                                         catcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGt                                               <  2:387406/141‑1 (MQ=255)

                                                                                          atcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTc                                              <  2:150235/141‑1 (MQ=255)

                                                                                               tACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGtgc                                         >  1:242289/1‑139 (MQ=255)

                                                                                                   ttttAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTgg                                     <  1:81781/141‑1 (MQ=255)

                                                                                                   ttttAAGTTAACAGGAGAGGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTgg                                     <  1:283866/141‑1 (MQ=255)

                                                                                                    tttAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGc                                    <  1:307002/141‑1 (MQ=255)

                                                                                                       aaGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGc                                 >  2:402450/1‑141 (MQ=255)

                                                                                                       aaGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATGTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGc                                 <  1:495304/141‑1 (MQ=255)

                                                                                                          ttAACAGGAGATGTGTCATACAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAGTTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCttt                              >  1:314157/1‑141 (MQ=255)

                                                                                                           tAACGGGGGATGTGTCATGCAATCAGGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTg                             <  2:359046/141‑1 (MQ=255)

                                                                                                             aCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGAc                           >  2:312027/1‑141 (MQ=255)

                                                                                                                  agaTGTGTCATGCAACCATGCGCCAAAACGTCAACAAATGCTAGATTTTAAAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACAtata                      <  1:249490/141‑1 (MQ=255)

                                                                                                                      gtgtCATGCAATCATGCGCCAAAACGACAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGa                  >  2:371557/1‑141 (MQ=255)

                                                                                                                               aaTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAata         <  2:423595/141‑1 (MQ=255)

                                                                                                                                aTCATGCGGCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCATTGGCCGCTGTGACATATACGGACCTCAAatat        >  2:393430/1‑141 (MQ=255)

                                                                                                                                aTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATGTACGGACCTCAAatat        >  2:240294/1‑141 (MQ=255)

                                                                                                                                 tCATGCGCCAACACGTCAACAACTGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGCCCTCAAATAtt       >  2:169354/1‑141 (MQ=255)

                                                                                                                                   aTGCGCCAAAACGTCAACAAATGATAGTTTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa     <  2:241931/141‑1 (MQ=255)

                                                                                                                                    tGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATATGGACCTCAAATATTAAt    >  2:494117/1‑141 (MQ=255)

                                                                                                                                      cgcCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAAtta  >  2:362711/1‑140 (MQ=255)

GGAGATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTC  >  CP000730/2855949‑2856223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A