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 835,918 C→T 21.1% I212I (ATC→ATT)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,9180CT21.1% 226.6 / 51.0 114I212I (ATC→ATT) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base C (39/50);  new base T (11/13);  total (50/64)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

Only 100 of 120 total aligned reads displayed.

CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTC  >  minE/835849‑835984
                                                                     |                                                                  
cccGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCg                                                                   <  1:4446315/71‑1 (MQ=255)
  cGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAc                                                                 <  1:2858466/71‑1 (MQ=255)
   ggCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                                                <  1:4683953/71‑1 (MQ=255)
        gcgtgGCGACCTGCCCAAGCGGCGCTATCTACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGa                                                            >  1:4385442/3‑70 (MQ=255)
         tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:456002/1‑70 (MQ=255)
         tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:2016248/1‑70 (MQ=255)
         tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:1775170/1‑70 (MQ=255)
         tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:4396349/1‑70 (MQ=255)
             gCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATaaa                                                        >  1:5052181/1‑69 (MQ=255)
                  cTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtg                                                 <  1:4317549/71‑1 (MQ=255)
                     cccGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtggc                                               <  1:512664/70‑1 (MQ=255)
                     cccAAGCGGCGCTATCTACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGtggc                                               <  1:2476477/70‑1 (MQ=255)
                       cGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtggctgg                                            >  1:5396429/1‑71 (MQ=255)
                         aGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCg                                          <  1:4305586/71‑1 (MQ=255)
                           cGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATg                                                      <  1:4212846/57‑1 (MQ=255)
                            ggTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAt                                       <  1:2869767/71‑1 (MQ=255)
                             gTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                                                <  1:3894254/45‑1 (MQ=255)
                              tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATa                                                          <  1:4264622/50‑1 (MQ=255)
                              tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtggc                                               <  1:2644161/61‑1 (MQ=255)
                              tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTa                                        <  1:1157081/68‑1 (MQ=255)
                              tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgt                                     <  1:3130205/71‑1 (MQ=255)
                              tGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATAGACCAGGATa                                                          <  1:4733414/50‑1 (MQ=255)
                               gCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgtg                                    >  1:3749414/1‑71 (MQ=255)
                               gCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgtg                                    >  1:3141955/1‑71 (MQ=255)
                                  aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                 <  1:4883487/71‑1 (MQ=255)
                                  aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                 <  1:3329174/71‑1 (MQ=255)
                                  aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                 <  1:2886675/71‑1 (MQ=255)
                                   tttACAAGCGTGAAGAAGATGGCATCGTCCTGATc                                                                    <  1:2013520/35‑1 (MQ=255)
                                   tttACAAGCGTGAAGAAGATGGCATCGTCCTGATc                                                                    <  1:821844/35‑1 (MQ=255)
                                   tttACAAGCGTGAAGAAGATGGCATCGTCCTGATc                                                                    <  1:1611923/35‑1 (MQ=255)
                                   tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATa                                                          <  1:3165576/45‑1 (MQ=255)
                                   tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATa                                                          <  1:262897/45‑1 (MQ=255)
                                   tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:564971/71‑1 (MQ=255)
                                   tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:371163/71‑1 (MQ=255)
                                   tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:870498/71‑1 (MQ=255)
                                   tctACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGtt                                        <  1:4137480/61‑2 (MQ=255)
                                    ctACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCAt                                 >  1:4756963/2‑69 (MQ=255)
                                     tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:2745206/69‑1 (MQ=255)
                                     tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:4979942/69‑1 (MQ=255)
                                     tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:2259651/69‑1 (MQ=255)
                                     tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                               <  1:1514189/70‑1 (MQ=255)
                                     tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                              >  1:5483122/1‑71 (MQ=255)
                                     tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                              >  1:5361167/1‑71 (MQ=255)
                                     tACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCAtaag                              >  1:3331763/1‑68 (MQ=255)
                                       cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                            <  1:2055133/71‑1 (MQ=255)
                                       cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                            <  1:5134126/71‑1 (MQ=255)
                                       cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                            <  1:1800628/71‑1 (MQ=255)
                                       cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                            <  1:1970781/71‑1 (MQ=255)
                                       cAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCAtaag                              <  1:1404041/69‑4 (MQ=255)
                                        aaGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTgg                           <  1:1942584/71‑1 (MQ=255)
                                          gCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATaa                                                         >  1:755488/1‑39 (MQ=255)
                                          gCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATaa                                                         >  1:903774/1‑39 (MQ=255)
                                          gCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtg                                      >  1:128815/1‑58 (MQ=255)
                                               aagaagATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCg                    <  1:1540661/71‑1 (MQ=255)
                                                agaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGtggc                                               >  1:3814929/1‑43 (MQ=255)
                                                agaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGtggc                                               >  1:64715/1‑43 (MQ=255)
                                                 gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGtg                                                 >  1:1698569/1‑40 (MQ=255)
                                                 gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                               >  1:1324929/1‑58 (MQ=255)
                                                 gaagaCGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGtt                                        >  1:1228482/1‑48 (MQ=255)
                                                 gaagaCGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGtt                                        >  1:5656719/1‑48 (MQ=255)
                                                     acggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTAaaaa              <  1:5016134/69‑1 (MQ=255)
                                                     aTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgt                                     <  1:3741857/48‑1 (MQ=255)
                                                      cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa             <  1:309817/70‑1 (MQ=255)
                                                        gCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaa           <  1:4788190/71‑1 (MQ=255)
                                                        gCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaa           <  1:386177/71‑1 (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                                      >  1:1471938/1‑39 (MQ=255)
                                                             gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtg                                      >  1:766584/1‑39 (MQ=255)
                                                             gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTTGATGCCCGTACAAAAAAATCTa      >  1:3125095/1‑71 (MQ=255)
                                                             gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCt       >  1:5307946/1‑70 (MQ=255)
                                                             gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa      <  1:1226672/71‑1 (MQ=255)
                                                             gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa      >  1:3710167/1‑71 (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)
                                                                cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                    <  1:2373668/38‑1 (MQ=25)
                                                                cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                    <  1:1542559/38‑1 (MQ=25)
                                                                cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                    <  1:5369587/38‑1 (MQ=25)
                                                                cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                    <  1:3140944/38‑1 (MQ=25)
                                                                cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACtt   <  1:4867959/71‑1 (MQ=255)
                                                                cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATCTACtt   >  1:363937/1‑71 (MQ=255)
                                                                cTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGAt                         >  1:1489037/1‑49 (MQ=255)
                                                                cTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGAt                         >  1:604633/1‑49 (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        <  1:259987/65‑1 (MQ=255)
                                                                 tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATc        <  1:3647417/65‑1 (MQ=255)
                                                                  gATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaaaa           >  1:1618407/1‑61 (MQ=255)
                                                                  gATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaaaa           >  1:4017352/1‑61 (MQ=255)
                                                                   aTCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTc  <  1:5626474/69‑1 (MQ=255)
                                                                     cGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                             >  1:2126145/1‑40 (MQ=255)
                                                                     cGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACt                             >  1:2304528/1‑40 (MQ=255)
                                                                     |                                                                  
CCCGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTC  >  minE/835849‑835984

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A