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 835,154 T→G 22.6% H1204Q (CAT→CAG)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1540TG22.6% 164.3 / 73.0 115H1204Q (CAT→CAG) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (39/50);  new base G (16/10);  total (55/60)
Fisher's exact test for biased strand distribution p-value = 1.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.80e-01

Only 100 of 119 total aligned reads displayed.

GTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGT  >  minE/835084‑835220
                                                                      |                                                                  
gtggtgGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                                    <  1:3182946/71‑1 (MQ=255)
gtggtgGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                                    <  1:3274302/71‑1 (MQ=255)
gtggtgGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                                    <  1:3347137/71‑1 (MQ=255)
  ggtggtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCt                                                                  >  1:5078199/1‑71 (MQ=255)
  ggtggtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCt                                                                  >  1:1600360/1‑71 (MQ=255)
      gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGc                                                               >  1:5168995/1‑70 (MQ=255)
      gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                              >  1:325779/1‑71 (MQ=255)
      gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                              >  1:2730619/1‑71 (MQ=255)
           cATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACg                                                          <  1:33495/70‑1 (MQ=255)
            aTAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGc                                                        >  1:1804288/1‑71 (MQ=255)
               aCTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                              <  1:2132096/62‑1 (MQ=255)
               aCTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                     <  1:5049240/71‑1 (MQ=255)
               aCTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCtt                                                      <  1:4279327/70‑1 (MQ=255)
               aCTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCt                                                       >  1:1977432/1‑69 (MQ=255)
               aCTCGGTCACCCGTATCACGCAGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                     <  1:1174669/71‑1 (MQ=255)
                 tCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGCCTATGCCCATCTGGCATACGGCttt                                                     <  1:1404137/69‑1 (MQ=255)
                  cGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAac                                                  >  1:5690437/1‑71 (MQ=255)
                    gTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                              <  1:3962265/57‑1 (MQ=255)
                       aCCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAActacta                                             >  1:4035309/1‑71 (MQ=255)
                         ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                           >  1:636062/1‑71 (MQ=255)
                           gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                                         <  1:4671923/71‑1 (MQ=255)
                           gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                                         <  1:3519468/71‑1 (MQ=255)
                             aTCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                                    >  1:2578909/1‑42 (MQ=255)
                              tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCGATCTGGCATACGGCTTTAACTACTATGGCAcc                                      >  1:2397428/1‑71 (MQ=255)
                              tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTgg                                                                <  1:4887088/45‑1 (MQ=255)
                              tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTgg                                                                <  1:874635/45‑1 (MQ=255)
                              tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTgg                                                                <  1:1957910/45‑1 (MQ=255)
                              tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                      >  1:916686/1‑71 (MQ=255)
                              tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                      >  1:5184292/1‑71 (MQ=255)
                                tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                    >  1:1028244/4‑71 (MQ=255)
                                tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                    >  1:3265087/4‑71 (MQ=255)
                                tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                    >  1:1140659/4‑71 (MQ=255)
                                tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                    >  1:757117/4‑71 (MQ=255)
                                aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAActacta                                             >  1:2769493/1‑62 (MQ=255)
                                aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                     <  1:4760013/70‑1 (MQ=255)
                                aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                     <  1:3495520/70‑1 (MQ=255)
                                aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                     <  1:659377/70‑1 (MQ=255)
                                aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                     >  1:5120562/1‑70 (MQ=255)
                                aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                    <  1:263755/71‑1 (MQ=255)
                                 gcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGtc                                   >  1:1715357/3‑70 (MQ=255)
                                  gCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                     <  1:2557802/52‑1 (MQ=255)
                                  gCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAg                                  <  1:829241/71‑1 (MQ=255)
                                   ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                    <  1:2645374/68‑1 (MQ=255)
                                   ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                    <  1:356987/68‑1 (MQ=255)
                                   ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                    <  1:4346845/68‑1 (MQ=255)
                                    cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                >  1:188003/1‑71 (MQ=255)
                                     gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                     <  1:4849503/49‑1 (MQ=255)
                                     gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                               >  1:936588/1‑71 (MQ=255)
                                     gAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCggat                               >  1:1957960/1‑69 (MQ=255)
                                     gAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCggat                               >  1:1801658/1‑69 (MQ=255)
                                      aaaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTc                              >  1:1058404/1‑71 (MQ=255)
                                       aaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTaa                                                   >  1:462480/1‑49 (MQ=255)
                                       aaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                             <  1:5628827/71‑1 (MQ=255)
                                       aaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATc                              >  1:2485470/1‑70 (MQ=255)
                                        aCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATcga                            <  1:1155060/71‑3 (MQ=255)
                                         ccaaCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGaa                           <  1:2363058/68‑1 (MQ=255)
                                           gACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                     <  1:3878354/43‑1 (MQ=255)
                                            aCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACcg                        >  1:194914/1‑71 (MQ=255)
                                             cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                       <  1:3139153/71‑1 (MQ=255)
                                             cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                       <  1:5627680/71‑1 (MQ=255)
                                                atatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt                    <  1:2074863/71‑1 (MQ=255)
                                                atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                    <  1:1623867/71‑1 (MQ=255)
                                                atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                    <  1:3939814/71‑1 (MQ=255)
                                                 tatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCGCCGtcg                                  <  1:1800593/56‑3 (MQ=255)
                                                 tatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGtcg                                  >  1:4731269/1‑54 (MQ=255)
                                                 tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                     <  1:3473633/37‑1 (MQ=255)
                                                 tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                     <  1:4150475/37‑1 (MQ=255)
                                                 tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                     <  1:737849/37‑1 (MQ=255)
                                                 tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                             <  1:1760513/61‑1 (MQ=255)
                                                 tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                             <  1:2636473/61‑1 (MQ=255)
                                                 tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                   <  1:387810/71‑1 (MQ=255)
                                                 tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                   <  1:5284471/71‑1 (MQ=255)
                                                  atGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                             <  1:3015777/60‑1 (MQ=255)
                                                   tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt                    >  1:480016/1‑68 (MQ=255)
                                                   tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg                   <  1:1093244/69‑1 (MQ=255)
                                                   tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGa                  <  1:3098752/70‑1 (MQ=255)
                                                   tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAg                 >  1:4471661/1‑71 (MQ=255)
                                                   tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTaa                                                   >  1:5210063/1‑37 (MQ=255)
                                                    gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt                >  1:1260521/1‑71 (MQ=255)
                                                    gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                     >  1:3139929/1‑50 (MQ=255)
                                                    gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                     >  1:3029433/1‑50 (MQ=255)
                                                    gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                     >  1:2545977/1‑50 (MQ=255)
                                                    gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                     >  1:2255828/1‑50 (MQ=255)
                                                    gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGt                >  1:2967366/1‑71 (MQ=255)
                                                      ttggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttc              <  1:3090538/69‑2 (MQ=255)
                                                       tggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttca             >  1:4320174/2‑69 (MQ=255)
                                                         gcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                    <  1:2652078/46‑1 (MQ=255)
                                                          cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg          <  1:3619986/71‑1 (MQ=255)
                                                          cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg          <  1:809850/71‑1 (MQ=255)
                                                             cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa        >  1:3173179/1‑70 (MQ=255)
                                                             cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACAGCGATGAGttt              >  1:4370012/1‑64 (MQ=255)
                                                              tATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt      >  1:235901/1‑71 (MQ=255)
                                                               aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgcg                      <  1:324015/54‑1 (MQ=255)
                                                                tGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttg             <  1:4504329/62‑1 (MQ=255)
                                                                  cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                             <  1:4788922/44‑1 (MQ=255)
                                                                  cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                             <  1:2125127/44‑1 (MQ=255)
                                                                  cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                           >  1:725216/1‑46 (MQ=255)
                                                                  cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt  <  1:140015/71‑1 (MQ=255)
                                                                   ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg       >  1:4510044/1‑65 (MQ=255)
                                                                   ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg       >  1:4361515/1‑65 (MQ=255)
                                                                      |                                                                  
GTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGT  >  minE/835084‑835220

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