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 835,921 C→T 21.8% D213D (GAC→GAT)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,9210CT21.8% 214.7 / 52.6 110D213D (GAC→GAT) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base C (41/45);  new base T (11/13);  total (52/58)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

Only 100 of 115 total aligned reads displayed.

CGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTC  >  minE/835851‑835984
                                                                      |                                                               
cGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAc                                                                 <  1:2858466/71‑1 (MQ=255)
 ggCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                                                <  1:4683953/71‑1 (MQ=255)
     tgcgtgGCGACCTGCCCAAGCGGCGCTATCTACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGa                                                            >  1:2592635/4‑71 (MQ=255)
       tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:1775170/1‑70 (MQ=255)
       tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:4396349/1‑70 (MQ=255)
       tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:456002/1‑70 (MQ=255)
       tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:2016248/1‑70 (MQ=255)
       tgtgGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGAt                                                           >  1:534635/1‑70 (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)
                           gTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                                                <  1:3645624/45‑1 (MQ=255)
                           gTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGAcc                                                                <  1:4924439/45‑1 (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)
                              cGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtgtg                                    >  1:5115664/1‑70 (MQ=255)
                                aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                 <  1:3329174/71‑1 (MQ=255)
                                aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                 <  1:4883487/71‑1 (MQ=255)
                                aTTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCAt                                 <  1:2886675/71‑1 (MQ=255)
                                 tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATa                                                          <  1:3165576/45‑1 (MQ=255)
                                 tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATa                                                          <  1:262897/45‑1 (MQ=255)
                                 tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:870498/71‑1 (MQ=255)
                                 tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:371163/71‑1 (MQ=255)
                                 tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:564971/71‑1 (MQ=255)
                                 tttACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:2778101/71‑1 (MQ=255)
                                  ctACAAACGCGAAGAAGACGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCAt                                 >  1:4756963/2‑69 (MQ=255)
                                   tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:2259651/69‑1 (MQ=255)
                                   tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:4979942/69‑1 (MQ=255)
                                   tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:4344729/69‑1 (MQ=255)
                                   tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                               >  1:4708042/1‑70 (MQ=255)
                                   tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                               <  1:1514189/70‑1 (MQ=255)
                                   tACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                              >  1:5483122/1‑71 (MQ=255)
                                     cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                            <  1:1970781/71‑1 (MQ=255)
                                     cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                            <  1:1800628/71‑1 (MQ=255)
                                     cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                            <  1:5134126/71‑1 (MQ=255)
                                     cAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTg                            <  1:2055133/71‑1 (MQ=255)
                                      aaGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTgg                           <  1:1942584/71‑1 (MQ=255)
                                       aGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtg                                                 >  1:1531544/1‑48 (MQ=255)
                                       aGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGtg                                                 >  1:2214513/1‑48 (MQ=255)
                                        gCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATaa                                                         >  1:755488/1‑39 (MQ=255)
                                        gCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTAtg                                      >  1:128815/1‑58 (MQ=255)
                                             aagaagATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCg                    <  1:1540661/71‑1 (MQ=255)
                                              agaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGtggc                                               >  1:64715/1‑43 (MQ=255)
                                              agaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGtggc                                               >  1:3814929/1‑43 (MQ=255)
                                               gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCa                               >  1:1324929/1‑58 (MQ=255)
                                               gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCAc                              >  1:704110/1‑59 (MQ=255)
                                               gaagaTGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTa                  >  1:3800940/1‑71 (MQ=255)
                                               gaagaCGGCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGtt                                        >  1:1228482/1‑48 (MQ=255)
                                                   acggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTAaaaa              <  1:5016134/69‑1 (MQ=255)
                                                    cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa             <  1:1296422/70‑1 (MQ=255)
                                                    cggCATTGTGCTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACaaaa             <  1:309817/70‑1 (MQ=255)
                                                      gCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACaaaaaa           <  1:386177/71‑1 (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       >  1:4170749/1‑70 (MQ=255)
                                                           gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCt       >  1:5307946/1‑70 (MQ=255)
                                                           gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa      <  1:172016/71‑1 (MQ=255)
                                                           gTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTa      >  1:3710167/1‑71 (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)
                                                              cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                    <  1:1542559/38‑1 (MQ=25)
                                                              cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                    <  1:5369587/38‑1 (MQ=25)
                                                              cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTtgtg                                    <  1:3140944/38‑1 (MQ=25)
                                                              cTGATTGATCAGGATAAATGCCGTGGCTGGCGTTTGTGCATAAGCGGTTGTCCGTACAAAAAAATc        >  1:5600705/1‑66 (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                                <  1:4979727/41‑1 (MQ=255)
                                                               tGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATc                                <  1:4282501/41‑1 (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)
                                                                      |                                                               
CGGCATGTGTGGCGACCTGCCCGAGCGGTGCGATTTACAAGCGTGAAGAAGATGGCATCGTCCTGATCGACCAGGATAAATGCCGTGGCTGGCGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTC  >  minE/835851‑835984

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