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
A19 F14 I0 R1	97	70.6	1554972	93.6%	1455453	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,343,438	C→T	48.7%	intergenic (+114/+250)	USA300HOU_2200 → / ← alsD	hypothetical protein/acetolactate decarboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,343,438	0	C	T	48.7%	0.0 / 72.8	60	intergenic (+114/+250)	USA300HOU_2200/alsD	hypothetical protein/acetolactate decarboxylase
Reads supporting (aligned to +/- strand): ref base C (12/18); new base T (10/19); total (22/38)
Fisher's exact test for biased strand distribution p-value = 7.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.70e-01

ATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGTAATT  >  CP000730/2343304‑2343574

ttACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTATCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGt                                                                                                                                    <  2:773137/140‑1 (MQ=255)

aTACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATataatata                                                                                                                                    >  2:438868/1‑139 (MQ=255)

aTACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTATCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGt                                                                                                                                    <  2:641337/141‑1 (MQ=255)

 tACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTa                                                                                                                                   >  1:413175/1‑141 (MQ=255)

 tACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTa                                                                                                                                   <  2:749326/141‑1 (MQ=255)

 tACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTAATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAACTTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTa                                                                                                                                   >  2:125778/1‑141 (MQ=255)

            gatAAATAATATTTTGAAAATATGTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACCTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATg                                                                                                                        <  1:118270/139‑1 (MQ=255)

                   aataatTCGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTCACATGAgtgtgt                                                                                                                 <  2:648403/141‑1 (MQ=255)

                    ataatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATCGTATATTTTATATGAgtgtgga                                                                                                                >  1:41630/1‑139 (MQ=255)

                        ttttAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTACTCAACTTGGAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACcac                                                                                                            <  1:367346/141‑1 (MQ=255)

                        tttGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACcac                                                                                                            <  2:332734/141‑1 (MQ=255)

                           gAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAAt                                                                                                         <  1:234114/141‑1 (MQ=255)

                             aaaTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAAttt                                                                                                       <  1:110337/141‑1 (MQ=255)

                             aaaTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAAttt                                                                                                       >  2:612975/1‑141 (MQ=255)

                              aaTGGTTTGATAGGGCAAGCGCTTAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTta                                                                                                      <  2:683466/141‑1 (MQ=255)

                              aaTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTta                                                                                                      >  1:619476/1‑141 (MQ=255)

                              aaTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTta                                                                                                      >  1:156501/1‑141 (MQ=255)

                                     ttATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTa                                                                                               >  2:753929/1‑141 (MQ=255)

                                       ataGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCGTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTaaa                                                                                             >  2:527404/1‑141 (MQ=255)

                                         aGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACa                                                                                           >  2:620195/1‑141 (MQ=255)

                                          gggCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACAt                                                                                          <  2:515199/141‑1 (MQ=255)

                                            gCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATAGGCCTATACCATAGTAAATATTATATGTGTGAGTACCACAATTaataataaaaccacaa                                                                                        >  1:159255/1‑131 (MQ=255)

                                            acAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATaa                                                                                        <  2:444640/140‑1 (MQ=255)

                                              aaGCGCTGAAAATTTCGCGTTTGTCTTTATAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACa                                                                                      <  2:697819/141‑1 (MQ=255)

                                                tcggttaaacaTTGGGCTTTGTCTTTCTAGTTAGTGACTCTGTAAACTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTCTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGc                                                                                    <  2:507095/135‑1 (MQ=255)

                                                  gcTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCaa                                                                                  <  1:546183/141‑1 (MQ=255)

                                                   cTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGGTTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACACTTTATAATGTAAACATAACAGaaaa                                                                                 >  2:292803/1‑141 (MQ=255)

                                                      aaaaaTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAAtct                                                                              <  2:73045/141‑1 (MQ=255)

                                                          aTTGGCGTTTTGCTTTTTAGTTATTGACCTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCaaa                                                                          <  1:636089/141‑1 (MQ=255)

                                                             ggCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAatat                                                                       <  1:624751/141‑1 (MQ=255)

                                                                      cTTTTTAGTTATTGAACTTGGAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCt                                                              <  1:423957/141‑1 (MQ=255)

                                                                              ttATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCACATCTCAAATATCTGGACCCTAATAAATc                                                      >  2:247539/1‑141 (MQ=255)

                                                                                 ttGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATcccc                                                   >  1:72343/1‑141 (MQ=255)

                                                                                  tGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCt                                                  <  2:775255/141‑1 (MQ=255)

                                                                                  tGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCt                                                  <  2:619476/141‑1 (MQ=255)

                                                                                  tGAACGTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCt                                                  <  2:156501/141‑1 (MQ=255)

                                                                                  tGAACGTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCt                                                  <  1:141423/141‑1 (MQ=255)

                                                                                   gAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTc                                                 <  1:483320/141‑1 (MQ=255)

                                                                                         gTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCaaaact                                           >  1:361294/1‑136 (MQ=255)

                                                                                          tAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTg                                          >  2:264962/1‑141 (MQ=255)

                                                                                          tAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTg                                          <  2:613650/141‑1 (MQ=255)

                                                                                          tAAAGTATGTTTGTTTGCTTCTCGTAGTAACAGATTGGCCTAGACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATTCCCTCACTACTg                                          <  1:400016/141‑1 (MQ=255)

                                                                                             attattGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTa                                       <  1:173099/141‑1 (MQ=255)

                                                                                                    ttgttTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGa                                >  2:653156/1‑141 (MQ=255)

                                                                                                      gttTTCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAACCATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAg                              <  2:69410/141‑1 (MQ=255)

                                                                                                      gttTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAg                              >  2:418439/1‑141 (MQ=255)

                                                                                                       tttGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAgg                             <  2:754792/141‑1 (MQ=255)

                                                                                                         tGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAACTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGa                           <  1:721488/141‑1 (MQ=255)

                                                                                                         tGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGa                           <  1:107846/141‑1 (MQ=255)

                                                                                                          gCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGat                          >  2:546689/1‑141 (MQ=255)

                                                                                                            ctctcGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAACCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGattt                        <  1:217178/140‑1 (MQ=255)

                                                                                                                 gtagtaACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGAtttatttt                   <  2:72343/141‑1 (MQ=255)

                                                                                                                   agtaACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGAtttattttat                 >  1:117196/1‑141 (MQ=255)

                                                                                                                    gtaACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACACAACAGCAAATCTCAATTAGCTGGGACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATttattttatt                <  1:527768/141‑1 (MQ=255)

                                                                                                                    gtaACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATttattttatt                >  1:23210/1‑141 (MQ=255)

                                                                                                                       aCAGATTGGCCTATATAACATTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACt             <  1:392811/141‑1 (MQ=255)

                                                                                                                       aCAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCACTCACTACTGCTAATCGTGACGGTATTTATTTTATTACt             >  2:398820/1‑141 (MQ=255)

                                                                                                                              tgCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGt      <  1:218182/140‑1 (MQ=255)

                                                                                                                              ggCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGt      <  1:16582/141‑1 (MQ=255)

                                                                                                                                ccTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTGATTACTTAGACGTaa    >  1:483940/1‑141 (MQ=255)

                                                                                                                                  cataAAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGTAAtt  <  1:471484/140‑1 (MQ=255)

ATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGTAATT  >  CP000730/2343304‑2343574

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