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 835,190 T→A 29.7% G1216G (GGT→GGA)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1900TA29.7% 203.1 / 112.8 141G1216G (GGT→GGA) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (41/58);  new base A (23/19);  total (64/77)
Fisher's exact test for biased strand distribution p-value = 1.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

Only 100 of 146 total aligned reads displayed.

CGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAT  >  minE/835120‑835259
                                                                      |                                                                     
cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                                       >  1:188003/1‑71 (MQ=255)
 gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                                      >  1:936588/1‑71 (MQ=255)
 gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                                      <  1:2364718/71‑1 (MQ=255)
  aaaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTc                                                                     >  1:1058404/1‑71 (MQ=255)
   aaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                                    <  1:5628827/71‑1 (MQ=255)
   aaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATcg                                                                    <  1:2752210/71‑2 (MQ=255)
   aaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATc                                                                     >  1:2485470/1‑70 (MQ=255)
     ccaaCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGaa                                                                  <  1:2363058/68‑1 (MQ=255)
        aCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACcg                                                               >  1:194914/1‑71 (MQ=255)
         cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                              <  1:3139153/71‑1 (MQ=255)
         cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                              <  1:5627680/71‑1 (MQ=255)
          gCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                              >  1:1627846/1‑70 (MQ=255)
             tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                                    <  1:1760513/61‑1 (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                                                          <  1:1835323/69‑1 (MQ=255)
               tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGa                                                         <  1:3098752/70‑1 (MQ=255)
               tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAg                                                        >  1:4471661/1‑71 (MQ=255)
               tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                                                        <  1:5188796/71‑1 (MQ=255)
                gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt                                                       >  1:805842/1‑71 (MQ=255)
                  ttggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttc                                                     <  1:4466787/69‑2 (MQ=255)
                  ttggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttc                                                     <  1:3090538/69‑2 (MQ=255)
                   tggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttca                                                    >  1:4320174/2‑69 (MQ=255)
                      cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                 <  1:3619986/71‑1 (MQ=255)
                      cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                 <  1:809850/71‑1 (MQ=255)
                         cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACAGCGATGAGttt                                                     >  1:4370012/1‑64 (MQ=255)
                           aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTATGTTCTAACcgcg                                                             <  1:3713206/54‑1 (MQ=255)
                           aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgcg                                                             <  1:324015/54‑1 (MQ=255)
                              cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                                    <  1:2125127/44‑1 (MQ=255)
                              cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                                    <  1:4788922/44‑1 (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)
                                    tGGCATCCGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                              >  1:731687/1‑60 (MQ=255)
                                    tGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                 >  1:3993820/1‑57 (MQ=255)
                                       cATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                                <  1:3865259/71‑1 (MQ=255)
                                       cATACGGCTTTAACTACTATGGCACCGTAGGTCCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                                <  1:3211259/71‑1 (MQ=255)
                                         tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                 <  1:4648466/52‑1 (MQ=255)
                                           cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGttt                                                     >  1:2608722/1‑46 (MQ=255)
                                           cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGttt                                                     >  1:1966182/1‑46 (MQ=255)
                                           cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGtt                                                      >  1:1204618/1‑45 (MQ=255)
                                           cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                               >  1:4306227/1‑52 (MQ=255)
                                           cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                               >  1:5170029/1‑52 (MQ=255)
                                           cGGCTTTAACTACTATGGCACCCTAGGTTCTAACCGCGa                                                            >  1:5509859/1‑39 (MQ=255)
                                             gCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                          <  1:2893467/71‑1 (MQ=255)
                                              cTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtta                         <  1:3280931/71‑2 (MQ=255)
                                               tttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtt                          <  1:2956660/69‑1 (MQ=255)
                                                ttAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGtt                                                      <  1:4224053/40‑1 (MQ=255)
                                                ttAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGtt                                                      <  1:4115027/40‑1 (MQ=255)
                                                  aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt                      <  1:3100500/70‑1 (MQ=255)
                                                  aaCTACTACGGCACCGTCGGATCGAACCGCGATGAGttc                                                     >  1:1521123/1‑38 (MQ=25)
                                                  aaCTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATgaagaa                              >  1:3456343/1‑62 (MQ=255)
                                                   actactATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                 <  1:3178041/42‑1 (MQ=255)
                                                   actactATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                 <  1:1108825/42‑1 (MQ=255)
                                                   actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAt                           >  1:3442705/1‑64 (MQ=255)
                                                   actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt                      <  1:5176581/69‑1 (MQ=255)
                                                   actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                    <  1:4961804/71‑1 (MQ=255)
                                                    ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                    <  1:4001945/70‑1 (MQ=255)
                                                    ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                   <  1:2812972/71‑1 (MQ=255)
                                                    ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                   <  1:105446/71‑1 (MQ=255)
                                                    ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc                   <  1:3275169/71‑2 (MQ=255)
                                                       ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                   >  1:4961987/1‑68 (MQ=255)
                                                         acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt              >  1:256060/3‑71 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                 >  1:1035745/1‑51 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                 >  1:1552395/1‑51 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa               <  1:5171278/69‑1 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa               <  1:1103606/69‑1 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa               <  1:1230388/69‑1 (MQ=255)
                                                          tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg             >  1:5242741/1‑71 (MQ=255)
                                                          cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcg                            >  1:1312757/2‑55 (MQ=255)
                                                          cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt              <  1:1590219/69‑1 (MQ=255)
                                                           ggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga            <  1:5684417/71‑2 (MQ=255)
                                                            gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat           >  1:3678124/1‑69 (MQ=255)
                                                            gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat           >  1:2619988/1‑69 (MQ=255)
                                                            gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat           >  1:227615/1‑69 (MQ=255)
                                                            gCACCGTCGGATCGAACCGCGATGACTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat           <  1:733046/71‑3 (MQ=255)
                                                            gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATgg            <  1:5495953/70‑1 (MQ=255)
                                                            gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATgg            <  1:5209487/70‑1 (MQ=255)
                                                             cACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat           >  1:3810990/1‑68 (MQ=255)
                                                             cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGc                                           <  1:1586383/38‑1 (MQ=255)
                                                             cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGTAGAACATTGACTGGTTAGATGGCg          <  1:2297451/71‑1 (MQ=255)
                                                             cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                >  1:5296291/1‑65 (MQ=255)
                                                             cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg          <  1:2319062/71‑1 (MQ=255)
                                                               ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg          >  1:2935844/1‑69 (MQ=255)
                                                                cGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                    <  1:3136321/58‑1 (MQ=255)
                                                                cGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                                         <  1:2258041/37‑1 (MQ=255)
                                                                 gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGa                                     >  1:4806926/1‑40 (MQ=255)
                                                                 gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGa                                     >  1:1300459/1‑40 (MQ=255)
                                                                 gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGGAGAACATTGACTGGTTa                 >  1:2039359/1‑60 (MQ=255)
                                                                 gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                 >  1:1116169/1‑60 (MQ=255)
                                                                  tAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                            >  1:3197425/1‑48 (MQ=255)
                                                                     gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                 <  1:1946457/56‑1 (MQ=255)
                                                                     gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                 <  1:5485123/56‑1 (MQ=255)
                                                                     gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt  <  1:959522/71‑1 (MQ=255)
                                                                     gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt  <  1:4239680/71‑1 (MQ=255)
                                                                      ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa         <  1:1123275/63‑1 (MQ=255)
                                                                      ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa         <  1:3286952/63‑1 (MQ=255)
                                                                      |                                                                     
CGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAT  >  minE/835120‑835259

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