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 835,376 A→G 38.3% S32G (AGC→GGC) ‡ narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,3760AG38.3% 96.9 / 130.3 128S32G (AGC→GGC) ‡narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base A (33/46);  new base G (22/27);  total (55/73)
Fisher's exact test for biased strand distribution p-value = 8.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.08e-01

Only 100 of 128 total aligned reads displayed.

GTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCGGGCCAGGGCTTCCC  >  minE/835310‑835440
                                                                  |                                                                
gTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCg                                                              <  1:696788/71‑1 (MQ=255)
  gCTGAATCTCGATAAGTGCATCGGCTGCCACAGCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                                             >  1:875915/1‑70 (MQ=255)
  gCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                                             >  1:4773351/1‑70 (MQ=255)
  gCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                                             >  1:4406792/1‑70 (MQ=255)
   cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                                             >  1:4223772/1‑69 (MQ=255)
   cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                                            <  1:4804319/70‑1 (MQ=255)
   cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                                            >  1:1232917/1‑70 (MQ=255)
   cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGa                                                           <  1:2550486/71‑1 (MQ=255)
      aacctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg                                                        >  1:5108994/4‑71 (MQ=255)
      aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa                                                          <  1:1816674/69‑1 (MQ=255)
       acctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg                                                        <  1:1544852/68‑1 (MQ=255)
       aTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTTAAGGc                                                       <  1:2791370/71‑1 (MQ=255)
        cctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGca                                                      <  1:1450542/70‑2 (MQ=255)
         ctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGcat                                                     <  1:3733652/71‑3 (MQ=255)
          tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAg                                                         >  1:4838527/1‑66 (MQ=255)
          tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc                                                       <  1:4108525/68‑1 (MQ=255)
          tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc                                                       <  1:1188328/68‑1 (MQ=255)
          tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc                                                       <  1:1833308/68‑1 (MQ=255)
            gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa                                                          >  1:225986/1‑63 (MQ=255)
            gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                                                   >  1:2555624/1‑70 (MQ=255)
            gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                                                   <  1:757757/70‑1 (MQ=255)
            gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                                                   <  1:2055536/70‑1 (MQ=255)
            gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                                                   >  1:5387749/1‑70 (MQ=255)
              tAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACAAGCCGTGAAGGCGTGGAat                                                <  1:5430758/71‑1 (MQ=255)
                aGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                                               <  1:5479613/70‑1 (MQ=255)
                 gTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATg                                             <  1:1222241/71‑1 (MQ=255)
                  tgtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGa                                                  >  1:1399268/4‑65 (MQ=255)
                  tGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGc                                            <  1:2175775/71‑1 (MQ=255)
                    taTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGcat                                          >  1:4991255/2‑69 (MQ=255)
                     aTCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTg                                         <  1:4955137/71‑1 (MQ=255)
                     aTCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTg                                         <  1:3262564/71‑1 (MQ=255)
                      tCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg                                                        <  1:4789916/55‑1 (MQ=255)
                      tCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                                            <  1:3297691/51‑1 (MQ=255)
                      tCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTgg                                        <  1:285264/71‑1 (MQ=255)
                        ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGt                                       <  1:2100921/70‑1 (MQ=255)
                        ggCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa                                                          >  1:2987253/1‑51 (MQ=255)
                        ggCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGt                                       >  1:2009209/1‑70 (MQ=255)
                             ccATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaaca                                 <  1:814686/71‑1 (MQ=255)
                              catacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaac                                  <  1:3604901/66‑1 (MQ=255)
                              catacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaac                                  <  1:4192014/66‑1 (MQ=255)
                              cacaCCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaacaa                                <  1:2951129/71‑1 (MQ=255)
                              cacaCCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaacaa                                <  1:3044269/71‑1 (MQ=255)
                                tacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGag                                                 <  1:2068490/51‑2 (MQ=255)
                                tacCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGag                                                 <  1:5557165/51‑2 (MQ=255)
                                cacCTGTTCAGTTACCTGTAAAAACGTCTGGCCCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg                              <  1:4458463/71‑1 (MQ=255)
                                cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg                              <  1:5591519/71‑1 (MQ=255)
                                 acCTGTTCGGCGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGttta                                    <  1:4527608/64‑3 (MQ=255)
                                 acCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAat                                                <  1:2963414/52‑1 (MQ=255)
                                 acCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGt                             >  1:5084967/1‑71 (MQ=255)
                                  ccTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAgta                                               >  1:5330937/1‑52 (MQ=255)
                                  ccTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGca                                           >  1:3193917/1‑55 (MQ=255)
                                  ccTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGtc                            >  1:3684700/1‑70 (MQ=255)
                                  ccTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGtc                            >  1:57590/1‑70 (MQ=255)
                                   cTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACTCATGGTTTAACAACGtc                            >  1:1973877/1‑69 (MQ=255)
                                    tGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGaa                                                          >  1:3467012/1‑39 (MQ=16)
                                    tGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGaa                                                          >  1:473428/1‑39 (MQ=16)
                                     gTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGag                                                 <  1:2268169/47‑2 (MQ=255)
                                      ttCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGaaa                        >  1:2403902/1‑71 (MQ=255)
                                      ttCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGaaa                        >  1:1289810/1‑71 (MQ=255)
                                      ttCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                                               >  1:4977295/1‑48 (MQ=255)
                                      ttCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGa                          <  1:1053184/69‑1 (MQ=255)
                                        cAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTc                                     >  1:2077286/1‑56 (MQ=255)
                                        cAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTc                                     >  1:4228091/1‑56 (MQ=255)
                                          gtgaCCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGAAACCaa                    <  1:3125305/68‑1 (MQ=255)
                                          gtgaCCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGAAACCaa                    <  1:2572197/68‑1 (MQ=255)
                                           ttACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAg                   >  1:1586002/1‑71 (MQ=255)
                                           ttACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAg                   >  1:5082360/1‑71 (MQ=255)
                                           ttACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAg                   >  1:3842573/1‑71 (MQ=255)
                                            tACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCg                                                      <  1:871703/35‑1 (MQ=255)
                                            gaCCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGAAACCaaac                  >  1:3144337/2‑69 (MQ=255)
                                             aCCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaac                                  >  1:1615938/1‑54 (MQ=255)
                                              ccTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCa                     <  1:314561/66‑1 (MQ=255)
                                                tGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCggg              >  1:5021954/1‑71 (MQ=255)
                                                 gTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaacaa                                >  1:4785181/1‑52 (MQ=255)
                                                 gTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGAAACCAAACCggg              >  1:3579405/1‑70 (MQ=255)
                                                 gTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaaca                                 <  1:4768250/51‑1 (MQ=255)
                                                 gTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaaca                                 <  1:1812442/51‑1 (MQ=255)
                                                 gTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGa                          >  1:2549367/1‑58 (MQ=255)
                                                 gTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGa                          >  1:1070581/1‑58 (MQ=255)
                                                 gTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCggg              >  1:65983/1‑70 (MQ=255)
                                                  tAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATg                                         <  1:353592/42‑1 (MQ=255)
                                                  tAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGAAACCAAACCggg              <  1:5453935/69‑1 (MQ=255)
                                                  tAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                                               >  1:5130005/1‑36 (MQ=255)
                                                  tAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                                               >  1:5629587/1‑36 (MQ=255)
                                                  tAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGa                          <  1:2172006/57‑1 (MQ=255)
                                                  tAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGa                          <  1:2614785/57‑1 (MQ=255)
                                                   aaaaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCaacaac                               >  1:3419345/1‑51 (MQ=255)
                                                   aaaaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCGGGc             >  1:763680/1‑69 (MQ=255)
                                                    aaaaCGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGt                             >  1:2524200/1‑52 (MQ=255)
                                                    aaaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaac                                  <  1:1976516/47‑1 (MQ=255)
                                                    aaaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCaa                    >  1:4597067/1‑61 (MQ=255)
                                                    aaaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCGGGCCAg          <  1:5291826/71‑1 (MQ=255)
                                                     aaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTg                            <  1:3860438/52‑1 (MQ=255)
                                                     aaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTg                            <  1:3669423/52‑1 (MQ=255)
                                                     aaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTg                            <  1:3225637/52‑1 (MQ=255)
                                                     aaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTg                            <  1:2925466/52‑1 (MQ=255)
                                                     aaaCGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCGGGCCa           <  1:1014431/69‑1 (MQ=255)
                                                       aCGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTTAACAACGTCGaaa                        >  1:1029114/1‑54 (MQ=255)
                                                         gTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCGGGCCAGGGCtt     >  1:1468629/1‑71 (MQ=255)
                                                              gACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCGGGCCAGGGCTTccc  <  1:116334/69‑1 (MQ=255)
                                                                  |                                                                
GTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACGTGGAAACCAAGCCGGGCCAGGGCTTCCC  >  minE/835310‑835440

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