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 2,919,564 A→G 13.3% T44T (ACT→ACC)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,5640AG13.3% 278.3 / 28.4 113T44T (ACT→ACC) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base A (46/52);  new base G (6/9);  total (52/61)
Fisher's exact test for biased strand distribution p-value = 7.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 114 total aligned reads displayed.

GCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTAACTGCAGC  >  minE/2919496‑2919627
                                                                    |                                                               
gCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAg                                                                >  1:2622028/1‑70 (MQ=255)
gCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGt                                                               >  1:4664973/1‑71 (MQ=255)
  ggCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGa                                                             <  1:3349754/71‑1 (MQ=255)
   gCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAg                                                            <  1:5144288/71‑1 (MQ=255)
   gCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAg                                                            <  1:499790/71‑1 (MQ=255)
    cAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAgc                                                           <  1:1253813/71‑2 (MQ=255)
       cTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTg                                                        <  1:701491/71‑1 (MQ=255)
       cTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTg                                                        <  1:2213201/71‑1 (MQ=255)
         tCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAGcttctg                                                      >  1:1113318/1‑68 (MQ=255)
           gAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGctt                                                    <  1:176865/71‑1 (MQ=255)
            aaaGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGtt                                                          <  1:3507232/64‑1 (MQ=255)
            aaaGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGtt                                                          <  1:5007830/64‑1 (MQ=255)
            aaaGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGtt                                                          <  1:1300597/64‑1 (MQ=255)
              agagCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttct                                                  >  1:1687932/1‑70 (MQ=255)
                agCATCTGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttc                                                <  1:5378828/70‑1 (MQ=255)
                 gCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttc                                                   >  1:1738901/1‑66 (MQ=255)
                    tCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGt                                                           <  1:3143502/55‑1 (MQ=255)
                     cGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGt                                                               >  1:3087559/1‑50 (MQ=255)
                     cGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGt                                                               >  1:4003619/1‑50 (MQ=255)
                     cGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGt                                                               >  1:2568902/1‑50 (MQ=255)
                     cGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGttt                                                         <  1:4079618/56‑1 (MQ=255)
                      gggTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttct                                                  >  1:163657/1‑62 (MQ=255)
                      gggTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCg                                         >  1:3633395/1‑71 (MQ=255)
                       ggTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGc                                        >  1:2542096/1‑71 (MQ=255)
                           cgagtcgagtCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCtttt                                    <  1:2151520/71‑1 (MQ=255)
                           cgagtcgagtCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCttt                                     <  1:1872522/70‑1 (MQ=255)
                               tcgagtcTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAg                                                            <  1:1699371/43‑1 (MQ=255)
                               tcgagtcTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttc                                                <  1:4788046/55‑1 (MQ=255)
                                 gagtcTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttcat                                              >  1:1111453/1‑53 (MQ=255)
                                  agtcTTTTTCGAAGATGAGCGCGATGTTTTTACCa                                                                 <  1:5544226/35‑1 (MQ=255)
                                  agtcTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATc                              <  1:4496425/70‑1 (MQ=255)
                                  agtcTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCg                             <  1:3189601/71‑1 (MQ=255)
                                   gtcTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTgg                                                       >  1:201510/1‑44 (MQ=255)
                                   gtcTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTgg                                                       >  1:42092/1‑44 (MQ=255)
                                    tcTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAGcttc                                                        <  1:395573/42‑2 (MQ=25)
                                    tcTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAGcttc                                                        <  1:3112486/42‑2 (MQ=25)
                                    tcTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGc                           <  1:892347/71‑1 (MQ=255)
                                      tttttCGAAGATGAGCGCGATGTTTTTTCCAGTGAGTTTGGCTTCTTCTTTACCGCttt                                     <  1:3720964/59‑1 (MQ=255)
                                      tttttCGAAGATGAGCGCGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCtt                         >  1:1066549/1‑71 (MQ=255)
                                      tttttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGct                                                     >  1:4191883/1‑43 (MQ=255)
                                      tttttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTAcc                                          <  1:4653121/54‑1 (MQ=255)
                                      tttttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTAc                                           >  1:1500129/1‑53 (MQ=255)
                                      tttttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCttt                                     <  1:3109575/59‑1 (MQ=255)
                                      tttttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCttt                                     <  1:836030/59‑1 (MQ=255)
                                        tttCGAAGATGAGCGCGATGTTTTTACCAGTGAGtt                                                          >  1:251679/1‑36 (MQ=255)
                                        tttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGc                                                      >  1:1683283/1‑40 (MQ=255)
                                        tttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGc                                        >  1:4436992/1‑54 (MQ=255)
                                        tttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATc                              >  1:2838773/1‑64 (MQ=255)
                                        tttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATc                              >  1:3489964/1‑64 (MQ=255)
                                        tttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCttt                        >  1:2972686/1‑70 (MQ=255)
                                        tttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCttt                        <  1:3048147/70‑1 (MQ=255)
                                        tttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCt                          <  1:3648799/68‑1 (MQ=255)
                                         ttCGAAGATGAGCGCGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCtttg                       <  1:4069147/70‑2 (MQ=255)
                                         ttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttctt                                              <  1:4276065/47‑1 (MQ=255)
                                         ttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCttt                        >  1:5548960/1‑69 (MQ=255)
                                         ttCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTc                       <  1:4869782/70‑1 (MQ=255)
                                          tCGAAGATGAGCGCGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCTTTGAg                     >  1:67537/1‑71 (MQ=255)
                                          tCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttctt                                              >  1:3784716/1‑46 (MQ=255)
                                            gAAGATGAGCGGGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCt                   <  1:3950715/71‑1 (MQ=255)
                                            gAAGATGAGCGCGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCTTTGAGCt                   <  1:1862618/71‑1 (MQ=255)
                                            gAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCa                      <  1:1361473/68‑1 (MQ=255)
                                            gAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCt                   <  1:3297626/71‑1 (MQ=255)
                                             aaGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCtt                  <  1:5082994/71‑1 (MQ=255)
                                             aaGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCATTCAGCtt                  <  1:4292735/71‑1 (MQ=255)
                                              aGATGAGCGCGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCTTTGAGCtgt                 >  1:3697866/1‑69 (MQ=255)
                                              aGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCtt                  <  1:3693964/70‑1 (MQ=255)
                                              aGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTc                 >  1:3863955/1‑71 (MQ=255)
                                               gATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTcg                <  1:3450634/71‑1 (MQ=255)
                                                aTGAGCGCGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCtttg                       <  1:3547569/63‑2 (MQ=255)
                                                 tGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTcgcg              >  1:1786043/1‑71 (MQ=255)
                                                 tGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTcgcg              >  1:3365949/1‑71 (MQ=255)
                                                   tgcgcGATTTTTTTACCAGTGAGTTTGGCTTCTTCttt                                             <  1:5185375/37‑1 (MQ=38)
                                                   aGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCtttt                                    >  1:4260061/1‑47 (MQ=255)
                                                   aGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTACTTTACCGCtttt                                    >  1:652379/1‑47 (MQ=255)
                                                    gcgcGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCt                          >  1:1133370/1‑56 (MQ=255)
                                                    gcgcGATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCTTTGAGCTGTGCGGca           <  1:246471/71‑2 (MQ=255)
                                                    gcgcGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCt           <  1:1198427/71‑1 (MQ=255)
                                                     cgcgATGTTTTTACCGGTAAGCTTCTGTACTTCCTTGCCATTTTTTTTATCGGCtttga                      >  1:2565545/1‑57 (MQ=255)
                                                      gcgATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTaa         <  1:1695396/71‑1 (MQ=255)
                                                      gcgATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTaa         <  1:5586578/71‑1 (MQ=255)
                                                      gcgATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTa          <  1:615408/70‑1 (MQ=255)
                                                          tGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCg                                         >  1:5546672/1‑35 (MQ=255)
                                                          tGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTAACTgc     <  1:5593071/71‑1 (MQ=255)
                                                          tGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTAACTg      >  1:4691741/1‑70 (MQ=255)
                                                           gTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGc                                        >  1:3147086/1‑35 (MQ=255)
                                                           gTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCa                      >  1:913339/1‑53 (MQ=255)
                                                           gTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCa                      >  1:2638289/1‑53 (MQ=255)
                                                           gTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTAACt       >  1:3403086/1‑68 (MQ=255)
                                                            tttttACCAGTGAGTTTGGCTTCTTCTTTACCGCtttt                                    <  1:5010164/38‑1 (MQ=255)
                                                            tttttACCAGTGAGTTTGGCTTCTTCTTTACCGCtttt                                    <  1:486361/38‑1 (MQ=255)
                                                             ttttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATc                              >  1:514493/1‑43 (MQ=255)
                                                             ttttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATc                              >  1:3951347/1‑43 (MQ=255)
                                                             ttttACCAGTGAGATTGGCTTCTTCTTTACCGCTTTTCTTATCGGCttta                       >  1:157661/1‑49 (MQ=255)
                                                              tttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCtt                                 >  1:2908816/1‑39 (MQ=255)
                                                              tttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCtt                                 >  1:266719/1‑39 (MQ=255)
                                                              tttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCtt                                 >  1:2322836/1‑39 (MQ=255)
                                                              tttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCttt                        >  1:1046939/1‑48 (MQ=255)
                                                              tttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGc                    >  1:1053741/1‑52 (MQ=255)
                                                              tttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTAACTgcagc  <  1:532089/70‑1 (MQ=255)
                                                              tttACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTAACTgcag   >  1:4765830/1‑69 (MQ=255)
                                                                    |                                                               
GCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTTTACCGCTTTTCTTATCGGCTTTCAGCTTCGCGGCTAACTGCAGC  >  minE/2919496‑2919627

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