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 835,956 C→G 29.2% T225S (ACT→AGT) ‡ narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,9560CG29.2% 125.4 / 64.3 89T225S (ACT→AGT) ‡narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base C (32/31);  new base G (15/11);  total (47/42)
Fisher's exact test for biased strand distribution p-value = 6.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01

TACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTA  >  minE/835886‑836025
                                                                      |                                                                     
tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                                                                       >  1:5361167/1‑71 (MQ=255)
tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                                                                       >  1:5483122/1‑71 (MQ=255)
  cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                                     <  1:2055133/71‑1 (MQ=255)
  cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                                     <  1:1970781/71‑1 (MQ=255)
  cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                                     <  1:1800628/71‑1 (MQ=255)
  cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                                     <  1:5134126/71‑1 (MQ=255)
   aaGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTgg                                                                    <  1:1942584/71‑1 (MQ=255)
          aagaagATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCg                                                             <  1:1540661/71‑1 (MQ=255)
            gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                                                                       >  1:704110/1‑59 (MQ=255)
            gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTa                                                           >  1:3800940/1‑71 (MQ=255)
                acggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTAaaaa                                                       <  1:5016134/69‑1 (MQ=255)
                 cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa                                                      <  1:1296422/70‑1 (MQ=255)
                 cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa                                                      <  1:309817/70‑1 (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                                                >  1:5307946/1‑70 (MQ=255)
                        gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCt                                                >  1:4170749/1‑70 (MQ=255)
                        gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                               >  1:3710167/1‑71 (MQ=255)
                        gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                               <  1:172016/71‑1 (MQ=255)
                        gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                               <  1:1226672/71‑1 (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                                            >  1:363937/1‑71 (MQ=255)
                           cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACtt                                            <  1:4867959/71‑1 (MQ=255)
                           cTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGAt                                                                  >  1:604633/1‑49 (MQ=255)
                           cTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGAt                                                                  >  1:1489037/1‑49 (MQ=255)
                           cTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACtt                                            >  1:3408598/1‑71 (MQ=255)
                            tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATc                                                 <  1:259987/65‑1 (MQ=255)
                            tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATc                                                 <  1:3647417/65‑1 (MQ=255)
                             gATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaaaa                                                    >  1:4017352/1‑61 (MQ=255)
                             gATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaaaa                                                    >  1:1618407/1‑61 (MQ=255)
                              aTCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTc                                           <  1:5626474/69‑1 (MQ=255)
                                cGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                                                                      >  1:2304528/1‑40 (MQ=255)
                                cGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                                                                      >  1:2126145/1‑40 (MQ=255)
                                    cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGa                                    >  1:4951460/1‑70 (MQ=255)
                                    cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGa                                    >  1:93115/1‑70 (MQ=255)
                                    cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGa                                    >  1:5075210/1‑70 (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                                           <  1:3073298/59‑1 (MQ=255)
                                        aTAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTc                                           <  1:408491/59‑1 (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                  <  1:1918336/71‑3 (MQ=255)
                                                     ctggcGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAgaaa                  <  1:3476060/71‑3 (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                <  1:1032385/65‑1 (MQ=255)
                                                             tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg                >  1:1602462/1‑65 (MQ=255)
                                                             tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg                >  1:4618052/1‑65 (MQ=255)
                                                             tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg                >  1:1521174/1‑65 (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                                  >  1:1217391/1‑44 (MQ=255)
                                                                gCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAag                                  >  1:4104112/1‑44 (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)
                                                                     aCTGGATGCCCGTACAAAAAAATCTACTTCAACTGGaa                                   >  1:2683843/1‑38 (MQ=255)
                                                                     aCTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCgg                             >  1:2012483/1‑44 (MQ=255)
                                                                     aCTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa  >  1:1327085/1‑71 (MQ=255)
                                                                     aCTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa  >  1:4679511/1‑71 (MQ=255)
                                                                      |                                                                     
TACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTA  >  minE/835886‑836025

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