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 835,946 A→T 28.7% M222L (ATG→TTG)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,9460AT28.7% 175.3 / 85.5 108M222L (ATG→TTG) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base A (32/45);  new base T (16/15);  total (48/60)
Fisher's exact test for biased strand distribution p-value = 3.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 109 total aligned reads displayed.

GGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGC  >  minE/835877‑836014
                                                                     |                                                                    
ggTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAt                                                                     <  1:2869767/71‑1 (MQ=255)
  tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTa                                                                      <  1:1157081/68‑1 (MQ=255)
  tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgt                                                                   <  1:3130205/71‑1 (MQ=255)
      aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                                               <  1:4883487/71‑1 (MQ=255)
      aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                                               <  1:3329174/71‑1 (MQ=255)
      aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                                               <  1:2886675/71‑1 (MQ=255)
       tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                              <  1:870498/71‑1 (MQ=255)
       tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                              <  1:564971/71‑1 (MQ=255)
       tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                              <  1:371163/71‑1 (MQ=255)
       tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                              <  1:2778101/71‑1 (MQ=255)
        ctACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCAt                                                               >  1:4756963/2‑69 (MQ=255)
         tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                              <  1:2745206/69‑1 (MQ=255)
         tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                              <  1:4344729/69‑1 (MQ=255)
         tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                              <  1:2259651/69‑1 (MQ=255)
         tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                                              <  1:4979942/69‑1 (MQ=255)
         tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                                                             <  1:1514189/70‑1 (MQ=255)
         tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                                                             >  1:4708042/1‑70 (MQ=255)
         tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                                                            >  1:5361167/1‑71 (MQ=255)
         tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                                                            >  1:5483122/1‑71 (MQ=255)
         tACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCAtaag                                                            >  1:3331763/1‑68 (MQ=255)
           cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                          <  1:1970781/71‑1 (MQ=255)
           cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                          <  1:2055133/71‑1 (MQ=255)
           cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                          <  1:5134126/71‑1 (MQ=255)
           cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                                                          <  1:1800628/71‑1 (MQ=255)
           cAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCAtaag                                                            <  1:1404041/69‑4 (MQ=255)
            aaGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTgg                                                         <  1:1942584/71‑1 (MQ=255)
              gCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtg                                                                    >  1:128815/1‑58 (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)
                         aTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgt                                                                   <  1:3741857/48‑1 (MQ=255)
                          cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa                                           <  1:309817/70‑1 (MQ=255)
                          cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa                                           <  1:1296422/70‑1 (MQ=255)
                            gCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaa                                         <  1:386177/71‑1 (MQ=255)
                            gCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaa                                         <  1:4788190/71‑1 (MQ=255)
                             cATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                                               <  1:3364544/48‑1 (MQ=255)
                              aTCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaaa                                        <  1:2707284/70‑1 (MQ=255)
                               tCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                                                           >  1:527203/1‑50 (MQ=255)
                               tCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                                                           >  1:527778/1‑50 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGGCGTGGCTGGCGTATGTGCATCACTGGa                                                        >  1:1190904/1‑51 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtg                                                                    >  1:3298731/1‑39 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtg                                                                    >  1:766584/1‑39 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtg                                                                    >  1:1471938/1‑39 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTTGATGCCCGTACAAAAAAATCTa                                    >  1:3125095/1‑71 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCt                                     >  1:5307946/1‑70 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCt                                     >  1:4170749/1‑70 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                    <  1:1226672/71‑1 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                    <  1:172016/71‑1 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                    >  1:2096562/1‑71 (MQ=255)
                                 gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                    >  1:3710167/1‑71 (MQ=255)
                                  tgcTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa                                           <  1:2870610/61‑1 (MQ=255)
                                  tCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa                                    <  1:5596636/70‑1 (MQ=255)
                                    cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                                                  <  1:2373668/38‑1 (MQ=25)
                                    cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                                                  <  1:5369587/38‑1 (MQ=25)
                                    cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                                                  <  1:3140944/38‑1 (MQ=25)
                                    cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                                                  <  1:1542559/38‑1 (MQ=25)
                                    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)
                                    cTGATCGACCAGGATAAATGACGTGGCTGGCGTAtg                                                                    >  1:2422380/1‑36 (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)
                                      gATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCa                                                                >  1:1703642/1‑38 (MQ=25)
                                      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                         >  1:5192835/1‑70 (MQ=255)
                                             cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGa                         >  1:5075210/1‑70 (MQ=255)
                                             cAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGa                         >  1:4951460/1‑70 (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                 <  1:768488/71‑2 (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                                       >  1:3078671/1‑41 (MQ=255)
                                                            ggctggcGTATGTGCATCACTGGATGCCCGTACAAAAAAAt                                       >  1:769644/1‑41 (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)
                                                                  cGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTg   >  1:5184138/1‑71 (MQ=255)
                                                                    tATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGc  <  1:1566502/70‑1 (MQ=255)
                                                                     |                                                                    
GGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGC  >  minE/835877‑836014

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