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 835,351 A→G 43.1% S23S (TCA→TCG)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,3510AG43.1% 62.8 / 161.3 137S23S (TCA→TCG) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base A (30/48);  new base G (29/30);  total (59/78)
Fisher's exact test for biased strand distribution p-value = 2.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 137 total aligned reads displayed.

ATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAA  >  minE/835283‑835418
                                                                    |                                                                   
   aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTTCCACACCTGTTCAGTTAc                                                                >  1:1753273/1‑71 (MQ=255)
   aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTa                                                                 <  1:2111745/70‑1 (MQ=255)
   aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAc                                                                >  1:2988737/1‑71 (MQ=255)
    aaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGAcc                                                               >  1:3033300/1‑71 (MQ=255)
     aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAcc                                                               <  1:5463800/70‑1 (MQ=255)
      aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAg                                                                    >  1:5531578/1‑64 (MQ=255)
       tccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGtg                                                                  <  1:2521365/63‑2 (MQ=255)
       tccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCt                                                              >  1:2955088/3‑69 (MQ=255)
          gTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaa                                                         <  1:39445/71‑1 (MQ=255)
          gTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaa                                                          <  1:4627365/70‑1 (MQ=255)
          gTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaa                                                          <  1:2735648/70‑1 (MQ=255)
           ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTTTaaaa                                                        <  1:1391440/71‑1 (MQ=255)
           ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaaaa                                                        <  1:823694/71‑1 (MQ=255)
           ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaaa                                                         <  1:2080557/70‑1 (MQ=255)
             cacaAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAAc                                                      >  1:2548851/1‑71 (MQ=255)
                aaGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaaa                                                        >  1:5685662/1‑66 (MQ=255)
                   tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                                                <  1:3266844/71‑1 (MQ=255)
                   tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                                                <  1:5621635/71‑1 (MQ=255)
                   tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTg                                                 <  1:4548543/70‑1 (MQ=255)
                     ggCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGAc                                              <  1:4918992/71‑1 (MQ=255)
                        aTGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGAccg                                            <  1:401755/70‑2 (MQ=255)
                           gTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCg                                        <  1:696788/71‑1 (MQ=255)
                             gCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTa                                                           >  1:921225/1‑50 (MQ=255)
                             gCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTa                                                           >  1:2454457/1‑50 (MQ=255)
                             gCTGAATCTCGATAAGTGCATCGGCTTCCACACCTGTTCAGTTACCTGTaa                                                          <  1:757831/51‑1 (MQ=255)
                             gCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                       >  1:4406792/1‑70 (MQ=255)
                             gCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                       >  1:4773351/1‑70 (MQ=255)
                              cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                      >  1:1232917/1‑70 (MQ=255)
                              cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGa                                     <  1:2550486/71‑1 (MQ=255)
                                 aacctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg                                  >  1:5108994/4‑71 (MQ=255)
                                 aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                      >  1:557873/1‑51 (MQ=255)
                                 aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                      >  1:290336/1‑51 (MQ=255)
                                 aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa                                    <  1:1816674/69‑1 (MQ=255)
                                   tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGt                                                                   <  1:2429816/36‑1 (MQ=255)
                                   tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCt                                                              >  1:1289996/1‑41 (MQ=255)
                                   tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                                                    <  1:4109947/51‑1 (MQ=255)
                                   tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                                                    <  1:3492849/51‑1 (MQ=255)
                                   tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                                                    <  1:2729899/51‑1 (MQ=255)
                                   cctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGca                                <  1:1450542/70‑2 (MQ=255)
                                   cctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGca                                <  1:3393405/70‑2 (MQ=255)
                                    ctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGcat                               <  1:3733652/71‑3 (MQ=255)
                                     tcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTa                                                                 >  1:690910/1‑36 (MQ=255)
                                     tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaa                                                         <  1:1253319/44‑1 (MQ=16)
                                     tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAg                                   >  1:4838527/1‑66 (MQ=255)
                                     tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc                                 <  1:1188328/68‑1 (MQ=255)
                                     tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc                                 <  1:4446910/68‑1 (MQ=255)
                                      cGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                                                 >  1:4888898/1‑51 (MQ=255)
                                       gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                             <  1:2055536/70‑1 (MQ=255)
                                       gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                             >  1:5387749/1‑70 (MQ=255)
                                       gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGCACCAGCCGTGAAGGCGTgg                             <  1:4789397/70‑1 (MQ=255)
                                        aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                      <  1:2184372/44‑1 (MQ=255)
                                        aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                      <  1:2326283/44‑1 (MQ=255)
                                        aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                      <  1:3557967/44‑1 (MQ=255)
                                         tAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACAAGCCGTGAAGGCGTGGAat                          <  1:5430758/71‑1 (MQ=255)
                                            gTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATg                       <  1:1222241/71‑1 (MQ=255)
                                             tGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGc                      <  1:2175775/71‑1 (MQ=255)
                                              gtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGt                                                    >  1:1063941/3‑40 (MQ=25)
                                              gtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGt                                                    >  1:5276277/3‑40 (MQ=25)
                                              gtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGt                                                    >  1:4808949/3‑40 (MQ=25)
                                              gtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGt                                                    >  1:2341640/3‑40 (MQ=25)
                                               taTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGcat                    >  1:4991255/2‑69 (MQ=255)
                                                aTCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTg                   <  1:4955137/71‑1 (MQ=255)
                                                 tCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg                                  <  1:4789916/55‑1 (MQ=255)
                                                 tCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                      <  1:3297691/51‑1 (MQ=255)
                                                 tCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTgg                  <  1:285264/71‑1 (MQ=255)
                                                 tCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTg                   >  1:3219286/1‑70 (MQ=255)
                                                   ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTg                                                 >  1:468651/1‑38 (MQ=25)
                                                   ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGtt                <  1:1970209/71‑1 (MQ=255)
                                                   ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGt                 <  1:2100921/70‑1 (MQ=255)
                                                   ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGt                 <  1:5213276/70‑1 (MQ=255)
                                                   ggCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGt                 >  1:2009209/1‑70 (MQ=255)
                                                     cTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTca              <  1:4868144/71‑1 (MQ=255)
                                                     cTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTca              <  1:1467275/71‑1 (MQ=255)
                                                        ccATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaaca           <  1:2643060/71‑1 (MQ=255)
                                                        ccATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaaca           <  1:814686/71‑1 (MQ=255)
                                                        ccACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaac            <  1:471589/70‑1 (MQ=255)
                                                         catacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaac            <  1:4192014/66‑1 (MQ=255)
                                                         catacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaac            <  1:3604901/66‑1 (MQ=255)
                                                         cacaCCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaacaa          <  1:2951129/71‑1 (MQ=255)
                                                         cacaCCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaacaa          <  1:3044269/71‑1 (MQ=255)
                                                           tacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGag                           <  1:170916/51‑2 (MQ=255)
                                                           tacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGag                           <  1:5557165/51‑2 (MQ=255)
                                                           cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg        >  1:4128877/1‑71 (MQ=255)
                                                            acCTGTTCGGCGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGttta              <  1:4527608/64‑3 (MQ=255)
                                                            acCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAat                          <  1:2963414/52‑1 (MQ=255)
                                                            acCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGt       >  1:5084967/1‑71 (MQ=255)
                                                             ccTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGca                     >  1:3193917/1‑55 (MQ=255)
                                                             ccTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGca                     >  1:63110/1‑55 (MQ=255)
                                                             ccTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGtc      >  1:3684700/1‑70 (MQ=255)
                                                             ccTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                      <  1:2062366/39‑1 (MQ=255)
                                                              cTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACTCATGGTTTAACAACGtc      >  1:1973877/1‑69 (MQ=255)
                                                               tGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGaa                                    >  1:3467012/1‑39 (MQ=16)
                                                                gTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGag                           <  1:2268169/47‑2 (MQ=255)
                                                                 ttCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGaaa  >  1:1289810/1‑71 (MQ=255)
                                                                 ttCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCg                                >  1:5080133/1‑41 (MQ=255)
                                                                 ttCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                         >  1:4977295/1‑48 (MQ=255)
                                                                 ttCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGa    <  1:1053184/69‑1 (MQ=255)
                                                                  tCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGaa                           <  1:963621/45‑1 (MQ=255)
                                                                   cAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTc               >  1:2077286/1‑56 (MQ=255)
                                                                   cAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTc               >  1:4228091/1‑56 (MQ=255)
                                                                    |                                                                   
ATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAA  >  minE/835283‑835418

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