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
A5 F1 I0 R2 201 99.6 7939938 96.9% 7693799 60.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,326 T→C 100% pseudogene (459/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3260TC97.4% 514.3 / 1.3 150pseudogene (459/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (4/0);  new base C (71/75);  total (75/75)
Fisher's exact test for biased strand distribution p-value = 1.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 157 total aligned reads displayed.

CGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGG  >  W3110S.gb/3824259‑3824393
                                                                   |                                                                   
cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc                                                                   <  1:1177173/70‑1 (MQ=255)
   gTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGGTGAAAACCAACCCGATg                                                               <  1:2218083/71‑1 (MQ=255)
    tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg                                                               >  1:1080058/1‑70 (MQ=255)
     gCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              >  1:4626179/1‑70 (MQ=255)
      ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa                                                             <  1:4128279/70‑1 (MQ=255)
      ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa                                                             <  1:2116255/70‑1 (MQ=255)
         gCGTGGCGCTGGAAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          >  1:3934252/1‑70 (MQ=255)
          cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:6426984/69‑1 (MQ=255)
          cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          <  1:4165145/69‑1 (MQ=255)
          cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                        <  1:6996063/71‑1 (MQ=255)
          cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                        >  1:5239686/1‑71 (MQ=255)
           gTGGCGCTGGCAGATGCGCTACAGCAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCg                                                                  >  1:5404963/1‑60 (MQ=255)
           gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCg                                                                  >  1:7556082/1‑60 (MQ=255)
           gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt                                                       <  1:1309421/71‑1 (MQ=255)
            tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                          >  1:4012229/1‑67 (MQ=255)
            tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt                                                       <  1:3033789/70‑1 (MQ=255)
            tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg                                                      <  1:4544927/71‑1 (MQ=255)
            tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg                                                      <  1:6316859/71‑1 (MQ=255)
             ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg                                                     >  1:2794583/1‑71 (MQ=255)
              gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                                    <  1:5896493/71‑1 (MQ=255)
               cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            <  1:2149409/62‑1 (MQ=255)
               cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            <  1:4865215/62‑1 (MQ=255)
                gcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa                                                   <  1:5320133/70‑1 (MQ=255)
                gcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa                                                   <  1:3462428/70‑1 (MQ=255)
                  tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg                                                      >  1:6246975/1‑65 (MQ=255)
                  tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc                                                >  1:2854874/1‑71 (MQ=255)
                  tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc                                                >  1:2408628/1‑71 (MQ=255)
                  tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc                                                >  1:5718457/1‑71 (MQ=255)
                      aGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAg                                            >  1:2871625/1‑71 (MQ=255)
                        aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              <  1:3944539/51‑1 (MQ=255)
                        aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGTGATGGTAGCCGCAGtt                                          >  1:1197409/1‑71 (MQ=255)
                        aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt                                                       <  1:6730234/58‑1 (MQ=255)
                          gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa                                                             >  1:4307616/1‑50 (MQ=255)
                          gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc                                        >  1:3698823/1‑71 (MQ=255)
                            gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              <  1:4320927/47‑1 (MQ=255)
                            gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              <  1:919136/47‑1 (MQ=255)
                             cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt                                     <  1:4713569/71‑1 (MQ=255)
                               aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAg                                                           >  1:5406049/1‑47 (MQ=255)
                               aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg                                   >  1:3517077/1‑71 (MQ=255)
                                 aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAggg                                                         <  1:5524740/47‑1 (MQ=255)
                                  gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc                                                >  1:2644366/1‑55 (MQ=255)
                                  gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta                                <  1:1102203/71‑3 (MQ=255)
                                   aaGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                              <  1:2704944/40‑1 (MQ=255)
                                     gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg                                                  <  1:1225835/50‑1 (MQ=255)
                                     gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                               >  1:3558915/1‑69 (MQ=255)
                                      cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                            >  1:3932608/1‑39 (MQ=255)
                                      cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgt                            <  1:4074926/71‑1 (MQ=255)
                                       tggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc                                        <  1:5482491/58‑1 (MQ=255)
                                         gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                         >  1:5092178/1‑71 (MQ=255)
                                          tggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg                             <  1:1427274/66‑1 (MQ=255)
                                           ggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg                                      >  1:2454315/1‑56 (MQ=255)
                                           ggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg                                      >  1:619202/1‑56 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                        >  1:1647026/1‑69 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                        >  1:5645881/1‑69 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                        >  1:5274513/1‑69 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                        >  1:274589/1‑69 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGc                                              <  1:4785275/47‑1 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                           >  1:6439135/1‑65 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                      <  1:5017540/71‑1 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                      >  1:5032618/1‑71 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                      >  1:3161862/1‑71 (MQ=255)
                                            gAAAACCGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                      >  1:7692046/1‑71 (MQ=255)
                                             aaaaCGGCTAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGc                                              <  1:2229184/46‑1 (MQ=39)
                                             aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg                                   <  1:4235103/57‑1 (MQ=255)
                                             aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                     <  1:3385571/71‑2 (MQ=255)
                                              aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                    <  1:6748580/71‑3 (MQ=255)
                                              aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                    <  1:6904795/71‑3 (MQ=255)
                                               aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGt                                           >  1:6180947/1‑47 (MQ=255)
                                               aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg                                   >  1:5843758/1‑55 (MQ=255)
                                               aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                    <  1:6588912/70‑3 (MQ=255)
                                               aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa                   <  1:6023278/71‑1 (MQ=255)
                                                aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc                                                 >  1:2970668/1‑40 (MQ=255)
                                                aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc                                                 >  1:2899328/1‑40 (MQ=255)
                                                aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                    >  1:7087252/1‑67 (MQ=255)
                                                 cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa                                                   <  1:585947/37‑1 (MQ=255)
                                                  ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                               <  1:204330/56‑1 (MQ=255)
                                                   gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                               <  1:6991481/55‑1 (MQ=255)
                                                   gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca               <  1:5139121/71‑2 (MQ=255)
                                                    cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa              >  1:7317590/1‑69 (MQ=255)
                                                       gCTGAAAACCAACACGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                           <  1:5557992/55‑2 (MQ=255)
                                                         tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt                                     >  1:6839142/1‑43 (MQ=255)
                                                         tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt                                     >  1:5884136/1‑43 (MQ=255)
                                                         tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                    >  1:2719626/1‑58 (MQ=255)
                                                         tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                     <  1:3551120/59‑2 (MQ=255)
                                                         tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg          >  1:283204/1‑70 (MQ=255)
                                                          gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                    >  1:6074585/1‑57 (MQ=255)
                                                          gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                    >  1:456254/1‑57 (MQ=255)
                                                           aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc         <  1:7254816/69‑1 (MQ=255)
                                                           aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa       >  1:1628997/1‑71 (MQ=255)
                                                           aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa       >  1:2190134/1‑71 (MQ=255)
                                                            aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCTAt      <  1:497281/71‑1 (MQ=255)
                                                            aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt      <  1:1508906/71‑1 (MQ=255)
                                                            aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt      >  1:7566278/1‑71 (MQ=255)
                                                             aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                       >  1:1849867/1‑53 (MQ=255)
                                                             aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc     <  1:1446023/71‑1 (MQ=255)
                                                               ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg   >  1:5948571/1‑71 (MQ=255)
                                                                cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg  <  1:253669/71‑1 (MQ=255)
                                                                cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg  <  1:827168/71‑1 (MQ=255)
                                                                cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg  <  1:4420449/71‑1 (MQ=255)
                                                                cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg   >  1:341934/1‑70 (MQ=255)
                                                                   |                                                                   
CGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGG  >  W3110S.gb/3824259‑3824393

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A