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
A6 F1 I2 R1	758	59.3	2864096	93.9%	2689386	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,664,363	(G)_6→7	coding (256/729 nt)	gadW ←	transcriptional activator of gadA and gadBC, repressor of gadX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,664,357	1	.	G	96.3%	188.6 / ‑0.1	54	coding (262/729 nt)	gadW	transcriptional activator of gadA and gadBC, repressor of gadX
Reads supporting (aligned to +/- strand): ref base . (1/1); new base G (25/27); total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.02e-01

TGCTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑GGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGC  >  NC_000913/3664219‑3664475

tGCTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAt                                                                                                                         <  2:356014/139‑1 (MQ=255)

  cTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑gg                                                                                                                      >  1:747676/1‑139 (MQ=255)

    aTTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑g                                                                                                                       <  2:627875/136‑1 (MQ=255)

    aTTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑g                                                                                                                       >  1:627875/1‑136 (MQ=255)

     ttGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑ggggg                                                                                                                   <  1:1140506/139‑1 (MQ=255)

        aaaaGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑gggggggt                                                                                                                >  1:1217611/1‑137 (MQ=255)

            gTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACt                                                                                                             <  2:747676/139‑1 (MQ=255)

            gTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACt                                                                                                             <  2:1217611/139‑1 (MQ=255)

               aGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGt                                                                                                          >  2:1424814/1‑139 (MQ=255)

                     tCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGttaatta                                                                                                    >  2:6155/1‑139 (MQ=255)

                       aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAt                                                                                                                         <  1:1068742/116‑1 (MQ=255)

                       aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAt                                                                                                                         >  2:1068742/1‑116 (MQ=255)

                       aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAAc                                                                                                  >  2:626928/1‑139 (MQ=255)

                          tctttcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACaaa                                                                                               <  1:1283304/139‑1 (MQ=255)

                           ctttcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAAc                                                                                              >  1:224561/1‑139 (MQ=255)

                              tcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGt                                                                                           >  2:670451/1‑139 (MQ=255)

                              tcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGt                                                                                           <  1:80445/139‑1 (MQ=255)

                              tcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGt                                                                                           >  1:1428550/1‑139 (MQ=255)

                                   tGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                      <  2:1428550/139‑1 (MQ=255)

                                   tGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                      >  2:1241833/1‑139 (MQ=255)

                                   tGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                      <  2:131586/139‑1 (MQ=255)

                                        aaaCATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                                 <  2:224561/139‑1 (MQ=255)

                                                        gAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                                 <  1:522153/123‑1 (MQ=255)

                                                        gAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                                 >  2:522153/1‑123 (MQ=255)

                                                        gAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑gggggggtga                                                                                                              >  1:570241/1‑89 (MQ=255)

                                                        gAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑gggggggtga                                                                                                              <  2:570241/93‑5 (MQ=255)

                                                        gAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑gggggggt                                                                                                                <  2:1353776/91‑3 (MQ=255)

                                                        gAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑gggggggt                                                                                                                >  1:1353776/1‑89 (MQ=255)

                                                                gagCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTg                                                         >  1:198672/1‑139 (MQ=255)

                                                                  gCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACaa                                                                                                >  2:991914/1‑98 (MQ=255)

                                                                  gCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACaa                                                                                                <  1:991914/98‑1 (MQ=255)

                                                                      atTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTgtgt                                                                                <  2:526948/110‑1 (MQ=255)

                                                                      atTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTgtgt                                                                                >  1:526948/1‑110 (MQ=255)

                                                                      atTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAat                                                   <  2:198672/139‑1 (MQ=255)

                                                                       ttGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAat                                                   >  1:984395/1‑138 (MQ=255)

                                                                       ttGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAat                                                   <  2:984395/138‑1 (MQ=255)

                                                                        tGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAatat                                                 >  1:696509/1‑139 (MQ=255)

                                                                           tCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAAtt                                                                     >  1:185506/1‑116 (MQ=255)

                                                                           tCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAAtt                                                                     <  2:185506/116‑1 (MQ=255)

                                                                               tATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTgtaa                                          >  2:483769/1‑139 (MQ=255)

                                                                                    gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAAt                                     >  1:1112780/1‑139 (MQ=255)

                                                                                    gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑gggggggtg                                                                                                               <  1:1170300/64‑4 (MQ=255)

                                                                                    gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑gggggggtg                                                                                                               >  2:1170300/1‑61 (MQ=255)

                                                                                         tttACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAAc                                                                                              <  1:69034/77‑1 (MQ=255)

                                                                                         tttACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAAc                                                                                              >  2:69034/1‑77 (MQ=255)

                                                                                         tttACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCaa                                <  1:1424814/139‑1 (MQ=255)

                                                                                              cccGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGt                           <  2:1112780/139‑1 (MQ=255)

                                                                                                       aTTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCtt                                                                                        <  2:408630/69‑1 (MQ=255)

                                                                                                       aTTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCtt                                                                                        >  1:408630/1‑69 (MQ=255)

                                                                                                       aTTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                                 >  2:289776/1‑76 (MQ=255)

                                                                                                       aTTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                                 <  1:289776/76‑1 (MQ=255)

                                                                                                          gAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑GGGGGGTGACTGGTTAATTAACAAACGGt                                                                                           >  1:1018093/1‑62 (MQ=255)

                                                                                                          gAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑GGGGGGTGACTGGTTAATTAACAAACGGt                                                                                           <  2:1018093/62‑1 (MQ=255)

                                                                                                            aGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAata                                                  <  2:146820/102‑1 (MQ=255)

                                                                                                            aGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAata                                                  >  1:146820/1‑102 (MQ=255)

                                                                                                             gCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGt                                                                                           >  1:519748/1‑60 (MQ=255)

                                                                                                             gCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGt                                                                                           <  2:519748/60‑1 (MQ=255)

                                                                                                             gCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATc            <  2:354871/139‑1 (MQ=255)

                                                                                                                aTCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAg         >  1:245100/1‑139 (MQ=255)

                                                                                                                 tCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAg                                                            <  1:948882/87‑1 (MQ=255)

                                                                                                                 tCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAg                                                            >  2:948882/1‑87 (MQ=255)

                                                                                                                 tCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATAtt                                                >  2:969236/1‑99 (MQ=255)

                                                                                                                 tCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATAtt                                                <  1:969236/99‑1 (MQ=255)

                                                                                                                 tCAAAAATCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAgt        <  2:696509/139‑1 (MQ=255)

                                                                                                                    aaaaTCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTCATTAACAAACGGTCTTTGCTGTGTAAACCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAgtcgt     <  1:868876/139‑1 (MQ=255)

                                                                                                                       aTCGCCGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTcgc  <  1:1241833/139‑1 (MQ=255)

                                                                                                                           ccGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGaa                                                    <  2:532265/85‑1 (MQ=255)

                                                                                                                           ccGTCACCAGCGGCATGGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGaa                                                    >  1:532265/1‑85 (MQ=255)

TGCTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑GGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGC  >  NC_000913/3664219‑3664475

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A