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 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	835,954	C→A	28.8%	I224I (ATC→ATA)	narH →	nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	835,954	0	C	A	28.8%	163.1 / 53.1	90	I224I (ATC→ATA)	narH	nitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand): ref base C (32/32); new base A (15/11); total (47/43)
Fisher's exact test for biased strand distribution p-value = 6.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01

Only 100 of 102 total aligned reads displayed.

TTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGC  >  minE/835884‑836023

tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:371163/71‑1 (MQ=255)

tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:870498/71‑1 (MQ=255)

tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:564971/71‑1 (MQ=255)

tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:2778101/71‑1 (MQ=255)

  tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:2745206/69‑1 (MQ=255)

  tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:2259651/69‑1 (MQ=255)

  tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:4979942/69‑1 (MQ=255)

  tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:4344729/69‑1 (MQ=255)

  tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                                                                      <  1:1514189/70‑1 (MQ=255)

  tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                                                                      >  1:4708042/1‑70 (MQ=255)

  tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                                                                     >  1:5483122/1‑71 (MQ=255)

  tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                                                                     >  1:5361167/1‑71 (MQ=255)

    cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                                   <  1:2055133/71‑1 (MQ=255)

    cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                                   <  1:1970781/71‑1 (MQ=255)

    cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                                   <  1:5134126/71‑1 (MQ=255)

    cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                                   <  1:1800628/71‑1 (MQ=255)

     aaGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTgg                                                                  <  1:1942584/71‑1 (MQ=255)

            aagaagATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCg                                                           <  1:1540661/71‑1 (MQ=255)

              gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                                                                      >  1:1324929/1‑58 (MQ=255)

              gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                                                                     >  1:704110/1‑59 (MQ=255)

              gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTa                                                         >  1:3800940/1‑71 (MQ=255)

                  acggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTAaaaa                                                     <  1:5016134/69‑1 (MQ=255)

                   cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa                                                    <  1:309817/70‑1 (MQ=255)

                   cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa                                                    <  1:1296422/70‑1 (MQ=255)

                     gCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaa                                                  <  1:4788190/71‑1 (MQ=255)

                     gCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaa                                                  <  1:386177/71‑1 (MQ=255)

                       aTCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaaa                                                 <  1:2707284/70‑1 (MQ=255)

                        tCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                                                                    >  1:527203/1‑50 (MQ=255)

                        tCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                                                                    >  1:527778/1‑50 (MQ=255)

                        tCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATc                                               <  1:1990543/71‑1 (MQ=255)

                          gTCCTGATCGACCAGGATAAATGGCGTGGCTGGCGTATGTGCATCACTGGa                                                                 >  1:1190904/1‑51 (MQ=255)

                          gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTTGATGCCCGTACAAAAAAATCTa                                             >  1:3125095/1‑71 (MQ=255)

                          gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCt                                              >  1:4170749/1‑70 (MQ=255)

                          gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCt                                              >  1:5307946/1‑70 (MQ=255)

                          gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                             <  1:1226672/71‑1 (MQ=255)

                          gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                             <  1:172016/71‑1 (MQ=255)

                          gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                             >  1:2096562/1‑71 (MQ=255)

                           tgcTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa                                                    <  1:2870610/61‑1 (MQ=255)

                           tCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                             <  1:5596636/70‑1 (MQ=255)

                             cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATc                                               >  1:5600705/1‑66 (MQ=255)

                             cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACtt                                          <  1:4867959/71‑1 (MQ=255)

                             cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACtt                                          >  1:363937/1‑71 (MQ=255)

                             cTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGAt                                                                >  1:604633/1‑49 (MQ=255)

                             cTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGAt                                                                >  1:1489037/1‑49 (MQ=255)

                             cTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACtt                                          >  1:3408598/1‑71 (MQ=255)

                              tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:4282501/41‑1 (MQ=255)

                              tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:5099237/41‑1 (MQ=255)

                              tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                                       <  1:4979727/41‑1 (MQ=255)

                              tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATc                                               <  1:3647417/65‑1 (MQ=255)

                              tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATc                                               <  1:259987/65‑1 (MQ=255)

                               gATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaaaa                                                  >  1:4017352/1‑61 (MQ=255)

                               gATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaaaa                                                  >  1:1618407/1‑61 (MQ=255)

                                aTCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTc                                         <  1:5626474/69‑1 (MQ=255)

                                  cGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                                                                    >  1:2126145/1‑40 (MQ=255)

                                  cGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                                                                    >  1:2304528/1‑40 (MQ=255)

                                      cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGa                                  >  1:5075210/1‑70 (MQ=255)

                                      cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGa                                  >  1:4951460/1‑70 (MQ=255)

                                      cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGa                                  >  1:5192835/1‑70 (MQ=255)

                                      cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGGCCGTACAAAAAAATCTACTTCAACTGGa                                  >  1:5557101/1‑70 (MQ=255)

                                      cAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTgg                                   >  1:3114638/1‑69 (MQ=255)

                                      cAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGaa                                 <  1:2101557/71‑1 (MQ=255)

                                       aGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGaa                                 >  1:1516311/1‑70 (MQ=255)

                                        ggATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAaga                               <  1:1550963/71‑1 (MQ=255)

                                          aTAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTc                                         <  1:408491/59‑1 (MQ=255)

                                          aTAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTc                                         <  1:3073298/59‑1 (MQ=255)

                                           tAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGc                             <  1:4141719/70‑1 (MQ=255)

                                           tAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCg                            <  1:5317603/71‑1 (MQ=255)

                                             aaTGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCggc                          <  1:4746770/71‑2 (MQ=255)

                                             aaTGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCggc                          <  1:768488/71‑2 (MQ=255)

                                              aTGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATc                                               >  1:4430594/1‑49 (MQ=255)

                                               tGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaaaa                                                  >  1:5000875/1‑45 (MQ=255)

                                                 ccGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGt                      >  1:1074032/1‑71 (MQ=255)

                                                   gTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCt                    <  1:1570587/71‑1 (MQ=255)

                                                     ggctggcGTATGTGCATCACTGGATGCCCGTACAAAAAAAt                                                >  1:769644/1‑41 (MQ=255)

                                                     ggctggcGTATGTGCATCACTGGATGCCCGTACAAAAAAAt                                                >  1:3078671/1‑41 (MQ=255)

                                                     ggctggcGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAaga                               <  1:854765/58‑1 (MQ=255)

                                                      tctggcGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAAt                                                >  1:468652/2‑40 (MQ=12)

                                                       ctggcGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAgaaa                <  1:3476060/71‑3 (MQ=255)

                                                       ctggcGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAgaaa                <  1:1918336/71‑3 (MQ=255)

                                                          gcGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTa                         <  1:5520125/59‑1 (MQ=255)

                                                          gcGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTa                         <  1:2745322/59‑1 (MQ=255)

                                                           cGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTg            >  1:5184138/1‑71 (MQ=255)

                                                             tATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGc           <  1:1566502/70‑1 (MQ=255)

                                                              ttgtgCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCAt         >  1:2078164/2‑71 (MQ=255)

                                                               tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAAc                                      >  1:3503882/1‑41 (MQ=255)

                                                               tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg              >  1:1602462/1‑65 (MQ=255)

                                                               tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg              >  1:1521174/1‑65 (MQ=255)

                                                               tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg              >  1:4618052/1‑65 (MQ=255)

                                                               tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg              <  1:1032385/65‑1 (MQ=255)

                                                               tgtgCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCAtc        >  1:2845228/1‑71 (MQ=255)

                                                               tgtgCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCAt         <  1:1071002/70‑1 (MQ=255)

                                                                 tgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGTTAAGTCTGAGAAGTGCAtct       <  1:573285/70‑1 (MQ=255)

                                                                 tgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCAtct       >  1:1468494/1‑70 (MQ=255)

                                                                  gCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAag                                >  1:4104112/1‑44 (MQ=255)

                                                                  gCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAag                                >  1:1217391/1‑44 (MQ=255)

                                                                   cATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGaa                                 >  1:5485886/1‑42 (MQ=255)

                                                                   cATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCAtcttct    <  1:1729687/71‑1 (MQ=255)

                                                                     tCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTg   <  1:4083360/70‑1 (MQ=255)

                                                                     tCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGc  <  1:4894376/71‑1 (MQ=255)

                                                                      cACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGc  >  1:4567232/1‑70 (MQ=255)

TTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGC  >  minE/835884‑836023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A