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
A1 F999 I1 R1 225 156.4 11709729 83.8% 9812752 75.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,548,005 C→T G701D (GGT→GAT)  malP ← maltodextrin phosphorylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,548,0050CT98.8% 498.6 / ‑6.2 162G701D (GGT→GAT) malPmaltodextrin phosphorylase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (71/89);  minor base G (1/1);  total (72/90)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 172 total aligned reads displayed.

TCGAAGGCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTACCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGACCA  >  NC_000913/3547933‑3548076
                                                                        |                                                                       
tCGAAGGCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCaccttatctt                                                                      <  1:2353468/76‑1 (MQ=255)
 cGAAGGCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCttt                                                                     <  2:3859117/76‑1 (MQ=255)
 cGAAGGCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCttt                                                                     <  1:3395686/76‑1 (MQ=255)
  gAAGGCATGCTTCTCGCCGTCTCTGTATTGACCGCTTTCCATCTCTTTCAATACTTCGTCCGTCACCTTATCTttc                                                                    <  1:1073126/76‑1 (MQ=255)
  gAAGGCATCATTATCGCCGTCCCTGTATTTACCGCTTTCCAGCGCTTTCAAGACTGCGTCCAGCACCTTATCTttc                                                                    <  1:4873254/76‑1 (MQ=255)
   aaGGCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTttct                                                                   <  1:974060/76‑1 (MQ=255)
   aaGGCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTttct                                                                   >  2:2659591/1‑76 (MQ=255)
    aGGCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTAtctttctt                                                                  <  1:4601100/76‑1 (MQ=255)
     ggCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTttcttc                                                                 <  2:4426602/76‑1 (MQ=255)
      gCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTcc                                                                <  1:3030092/76‑1 (MQ=255)
        aTGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGc                                                              >  2:3353108/1‑76 (MQ=255)
        aTGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGc                                                              >  2:3367383/1‑76 (MQ=255)
        aTGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGc                                                              >  1:4961396/1‑76 (MQ=255)
        aTGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGc                                                              <  1:3896524/76‑1 (MQ=255)
         tGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATGCTGCGTCCAGCACCTTATCTTTCTTCCGcc                                                             <  2:2406747/76‑1 (MQ=255)
         tGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGcc                                                             >  1:3110855/1‑76 (MQ=255)
          gCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCa                                                            >  1:481758/1‑76 (MQ=255)
           cTTATCGCCTGCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCAt                                                           <  2:5287866/76‑1 (MQ=255)
            ttATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCCtt                                                          >  2:5314520/1‑76 (MQ=255)
             tATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCAttt                                                         <  2:4840315/76‑1 (MQ=255)
             tATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCAttt                                                         <  2:5602677/76‑1 (MQ=255)
             tATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCAttt                                                         >  2:44273/1‑76 (MQ=255)
              aTCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTc                                                        <  1:1783365/76‑1 (MQ=255)
               tCGCCGTCGCTGTATTTACCGCTTTCCATCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCa                                                       <  2:4672006/76‑1 (MQ=255)
               tCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCa                                                       <  2:2660375/76‑1 (MQ=255)
               tCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCa                                                       >  2:4560300/1‑76 (MQ=255)
               tCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTCTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCa                                                       <  2:724447/76‑1 (MQ=255)
                cGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCAc                                                      >  2:2410026/1‑76 (MQ=255)
                cGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCAc                                                      >  2:5077029/1‑76 (MQ=255)
                 gCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCAcc                                                     >  1:3509333/1‑76 (MQ=255)
                  ccGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCg                                                    <  2:3553420/76‑1 (MQ=255)
                   cGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCgg                                                   <  1:1838016/76‑1 (MQ=255)
                    gTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCggg                                                  >  2:2273721/1‑76 (MQ=255)
                    gTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCggg                                                  >  2:2808810/1‑76 (MQ=255)
                     tCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCAt                                                           >  1:3339581/1‑66 (MQ=255)
                     tCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGt                                                 <  2:1661884/76‑1 (MQ=255)
                     tCGCTGGATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGt                                                 >  2:5549630/1‑76 (MQ=255)
                      cGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTc                                                >  1:5436106/1‑76 (MQ=255)
                       gCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCg                                               <  1:168649/76‑1 (MQ=255)
                       gCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCg                                               >  1:2680899/1‑76 (MQ=255)
                         tGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTa                                             >  2:3501740/1‑76 (MQ=255)
                         tGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTa                                             <  1:3520511/76‑1 (MQ=255)
                         tGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTa                                             <  1:1104198/76‑1 (MQ=255)
                           tATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGc                                           >  2:3034760/1‑76 (MQ=255)
                           tATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGc                                           <  1:3099764/76‑1 (MQ=255)
                           tATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGc                                           <  2:2512073/76‑1 (MQ=255)
                            aTTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGcc                                          <  1:597364/76‑1 (MQ=255)
                             tttACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCt                                         >  2:4187067/1‑76 (MQ=255)
                             tttACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTATTCCGCCATTTCACAGGGTCGTAGCCt                                         >  1:1038847/1‑76 (MQ=255)
                              ttACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCTTAGCCtt                                        >  1:619270/1‑76 (MQ=255)
                               tACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCttt                                       <  1:1389715/76‑1 (MQ=255)
                               tACCGCTTCCCAGCTCTTCCAATCCGGCGCCGAGCCCCGTATCTGTCCACCGCCATGTCCCCGGGTCGTAGCCgtt                                       <  2:1511979/76‑1 (MQ=255)
                                 ccGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTgg                                     <  1:5670707/76‑1 (MQ=255)
                                   gCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGcc                                   >  2:3896400/1‑76 (MQ=255)
                                   gCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGcc                                   >  2:412804/1‑76 (MQ=255)
                                     tttCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAg                                 >  1:4559371/1‑76 (MQ=255)
                                      tcccAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGa                                <  2:1266082/74‑1 (MQ=255)
                                       tCCAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCACTTCACCGGGTCGTAGCCTTTGGCCAGaa                               <  1:5378376/76‑1 (MQ=255)
                                        ccAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAAt                              >  2:1712437/1‑76 (MQ=255)
                                        ccAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAAt                              <  1:12143/76‑1 (MQ=255)
                                         cAGCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAAtt                             <  1:1324651/76‑1 (MQ=255)
                                           gCTCTTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGc                           <  2:1057523/76‑1 (MQ=255)
                                             tctTTCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCt                         >  2:3315403/1‑76 (MQ=255)
                                               tttCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTc                       >  1:1932583/1‑76 (MQ=255)
                                               tttCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTc                       <  2:4289580/76‑1 (MQ=255)
                                               tttCAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTc                       <  1:2681462/76‑1 (MQ=255)
                                                  cAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACt                    <  2:3548266/76‑1 (MQ=255)
                                                  cAATACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACt                    >  2:2673082/1‑76 (MQ=255)
                                                   aaTACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACtt                   >  2:4879246/1‑76 (MQ=255)
                                                   aaTACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACtt                   <  1:4775036/76‑1 (MQ=255)
                                                   aaTACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACtt                   <  1:2863478/76‑1 (MQ=255)
                                                    aTACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTg                  <  2:920973/76‑1 (MQ=255)
                                                    aTACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTg                  >  1:5301153/1‑76 (MQ=255)
                                                     tACTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGt                 <  1:1635265/76‑1 (MQ=255)
                                                      aCTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGtt                <  1:2273721/76‑1 (MQ=255)
                                                       cTGCGTCCAGCACCTTATCTTTCTTCCTCCATTTCACCGTGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTc               <  1:1843038/76‑1 (MQ=255)
                                                       cTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTc               <  1:672772/76‑1 (MQ=255)
                                                       cTGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTc               >  2:2150917/1‑76 (MQ=255)
                                                        tGCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTcc              <  2:1170303/76‑1 (MQ=255)
                                                         gCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCa             >  2:1551434/1‑76 (MQ=255)
                                                         gCGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCa             <  1:2410026/76‑1 (MQ=255)
                                                         gCGGCCAGCACGTTAGCGTGCTTCCGCCATTTCGCGGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCa             <  2:600986/76‑1 (MQ=255)
                                                          cGTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCAc            <  2:1039288/76‑1 (MQ=255)
                                                           gTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACg           >  1:4124252/1‑76 (MQ=255)
                                                           gTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACg           >  1:1488153/1‑76 (MQ=255)
                                                           gTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACg           >  2:5459123/1‑76 (MQ=255)
                                                           gTCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACg           <  1:5387884/76‑1 (MQ=255)
                                                           gTCCAGCACCTTATCTTGCTGCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACg           <  2:363182/76‑1 (MQ=255)
                                                            tCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACg           >  2:4162518/1‑75 (MQ=255)
                                                            tCCAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACg           <  1:4162519/75‑1 (MQ=255)
                                                             ccAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGt         <  2:1129201/76‑1 (MQ=255)
                                                             ccAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGt         <  1:1257575/76‑1 (MQ=255)
                                                              cAGCACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGACAGAATTGCCTTCACTTGTTCCACGGTa        >  1:2253129/1‑76 (MQ=255)
                                                                 cACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGa     >  2:1903929/1‑76 (MQ=255)
                                                                 cACCTTATCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGa     >  1:1228429/1‑76 (MQ=255)
                                                                  accttatcttTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGAc    >  1:1754718/1‑76 (MQ=255)
                                                                  accttatcttTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGAc    >  1:1390192/1‑76 (MQ=255)
                                                                   ccttatcttTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGAcc   <  2:1889951/76‑1 (MQ=255)
                                                                   acttatcgtTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGAcc   <  1:3194537/75‑1 (MQ=255)
                                                                    cttatcttTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGACCa  >  1:760707/1‑76 (MQ=255)
                                                                        |                                                                       
TCGAAGGCATGCTTATCGCCGTCGCTGTATTTACCGCTTTCCAGCTCTTTCAATACTGCGTCCAGCACCTTACCTTTCTTCCGCCATTTCACCGGGTCGTAGCCTTTGGCCAGAATTGCCTTCACTTGTTCCACGGTATGACCA  >  NC_000913/3547933‑3548076

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A