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
A11 F212 I1 R1 174 80.0 3892211 96.7% 3763768 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,500,814 Δ1 bp intergenic (‑23/‑446) yjgX ← / → yjgZ pseudogene fragment/uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,500,8110T.97.0% 293.1 / 2.2 67intergenic (‑20/‑449)yjgX/yjgZpseudogene fragment/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base . (27/38);  total (28/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

GTCCGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGTTTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGCAAGAGGGGGCCT  >  NC_000913/4500712‑4500909
                                                                                                   |                                                                                                  
gtCCGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAgtgt                                                                                                    >  1:1472442/1‑100 (MQ=255)
 tCCGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGtt                                                                                                   <  1:164711/100‑1 (MQ=255)
  ccGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGttt                                                                                                  >  1:372118/1‑100 (MQ=255)
   cGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGtttc                                                                                                 >  1:918402/1‑99 (MQ=255)
   cGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGtttc                                                                                                 >  1:1842286/1‑99 (MQ=255)
   cGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGtttc                                                                                                 >  1:502285/1‑99 (MQ=255)
   cGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGtttc                                                                                                 <  1:1632374/100‑2 (MQ=255)
    gCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGtttct                                                                                                <  2:410399/100‑3 (MQ=255)
      cAGAACATCACCAGGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAATCACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGtttctg                                                                                               <  1:155336/99‑4 (MQ=255)
      cAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGtttctgt                                                                                              >  1:142910/1‑96 (MQ=255)
       aGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTa                                                                                            <  1:148208/100‑1 (MQ=255)
       aGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTa                                                                                            <  2:907443/100‑1 (MQ=255)
         aaatTCACCACGAATACCAGAATCTCGGCACTGACCAGAAAATGTTAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAgg                                                                                          <  1:9015/100‑1 (MQ=255)
           aaTCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGtt                                                                                        <  2:455637/100‑1 (MQ=255)
              caccacGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTg                                                                                     <  2:757029/100‑1 (MQ=255)
               accacGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGa                                                                                    >  1:767637/1‑100 (MQ=255)
               accacGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGa                                                                                    >  1:1274808/1‑100 (MQ=255)
                ccacGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTg                                                                                     <  1:629040/98‑1 (MQ=255)
                ccacGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGaa                                                                                   <  1:20772/100‑1 (MQ=255)
                ccacGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGaa                                                                                   <  1:20670/100‑1 (MQ=255)
                  acGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAAcc                                                                                 <  2:372120/100‑1 (MQ=255)
                  acGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAAcc                                                                                 <  2:1615990/100‑1 (MQ=255)
                  acGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAAcc                                                                                 <  1:1287465/100‑1 (MQ=255)
                        aCCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCt                                                                           >  2:788841/1‑100 (MQ=255)
                        aCCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCt                                                                           <  1:982495/100‑1 (MQ=255)
                        aCCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTCCt                                                                           >  2:1545008/1‑100 (MQ=255)
                          cAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAg                                                                         >  1:272832/1‑100 (MQ=255)
                               tCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCgggg                                                                    <  2:278924/100‑1 (MQ=255)
                               tCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCgggg                                                                    <  2:1736560/100‑1 (MQ=255)
                                cgcgGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGt                                                                   >  2:583515/1‑100 (MQ=255)
                                 gcgGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGtt                                                                  <  2:263072/100‑1 (MQ=255)
                                   ggCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTtgt                                                                >  2:946531/1‑100 (MQ=255)
                                     cACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGa                                                              >  2:1104377/1‑100 (MQ=255)
                                      aCTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAg                                                             <  2:1130691/100‑1 (MQ=255)
                                       cTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAgg                                                            <  1:1506252/100‑1 (MQ=255)
                                        tGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGc                                                           >  2:1478891/1‑100 (MQ=255)
                                         gACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCt                                                          >  1:509243/1‑100 (MQ=255)
                                           ccAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGa                                                        >  2:1379042/1‑100 (MQ=255)
                                             aGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATg                                                      <  2:1492239/100‑1 (MQ=255)
                                              gAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATgg                                                     <  2:415364/100‑1 (MQ=255)
                                              gAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATgg                                                     >  2:1473565/1‑100 (MQ=255)
                                                      tAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGcc                                             >  2:963128/1‑100 (MQ=255)
                                                        aaCAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCgg                                           >  2:1923094/1‑100 (MQ=255)
                                                        aaCAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCgg                                           <  2:1335634/100‑1 (MQ=255)
                                                          cAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGc                                         >  1:258753/1‑100 (MQ=255)
                                                          cAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGc                                         <  1:1788115/100‑1 (MQ=255)
                                                          cAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGc                                         <  2:1039917/100‑1 (MQ=255)
                                                          cAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGc                                         <  1:1392702/100‑1 (MQ=255)
                                                           aGGAAACACGGGGCTGTTCACTTTGCTTTCTCCTGTAGTGTTTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGc                                         <  2:159060/100‑1 (MQ=255)
                                                             gAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGAG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGctct                                      >  2:1368134/1‑100 (MQ=255)
                                                             gAAACACGGGCCGGCTCACTCTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGCTCTAGCGGCGTTGTGAGGCTGATGGCAATCGc                                              >  1:1780116/1‑92 (MQ=255)
                                                                acacGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTcc                                   <  2:502287/100‑1 (MQ=255)
                                                                 cacGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCt                                  >  2:783789/1‑100 (MQ=255)
                                                                  acGGGGCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTg                                 <  2:142911/100‑1 (MQ=255)
                                                                    ggggCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGc                                >  1:1604169/1‑99 (MQ=255)
                                                                     gggCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCa                               >  2:1496781/1‑99 (MQ=255)
                                                                      ggCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATg                             <  2:1472450/100‑1 (MQ=255)
                                                                      ggCGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCCTAACCGGTTCTAGCGGGGTCGTGAGGCTGATGGCAATCGCCGAGCTCTTCCTGCATg                             <  2:29150/100‑1 (MQ=255)
                                                                        cGGTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGtt                           >  2:87348/1‑100 (MQ=255)
                                                                        cGGTTCACTTTGCTTTCTCCTGAAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGCTGGCAATCGCCGGGCTCTTCCTGCATGtt                           >  1:1478429/1‑100 (MQ=255)
                                                                          gTTCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTac                         <  2:1611586/100‑1 (MQ=255)
                                                                            tCACTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTacac                       <  2:1369512/100‑1 (MQ=255)
                                                                              aCTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTg                     >  1:1817558/1‑100 (MQ=255)
                                                                               cTTTGCTTTCTCCTGTAGTGTTTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTg                     >  2:372434/1‑100 (MQ=255)
                                                                               cTTTGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTgg                    <  2:545051/100‑1 (MQ=255)
                                                                                  tGCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTa                  <  2:279646/99‑1 (MQ=255)
                                                                                  agCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTAc                 <  2:825046/99‑1 (MQ=255)
                                                                                   gCTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACt                >  2:681420/1‑100 (MQ=255)
                                                                                    cTTTCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTg               <  1:1251182/100‑1 (MQ=255)
                                                                                     tttCTCCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGc              <  2:431398/100‑1 (MQ=255)
                                                                                        ctcCTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGCAag           <  2:1260743/100‑1 (MQ=255)
                                                                                          ccTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGCAagag         >  1:1789972/1‑100 (MQ=255)
                                                                                          ccTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCCCTTCCTGCATGTTACACTGGTACTGCAagag         >  1:582438/1‑100 (MQ=255)
                                                                                           cTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGCAAGAgg        <  2:1842298/100‑1 (MQ=255)
                                                                                           cTGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGCAAGAgg        <  2:1413937/100‑1 (MQ=255)
                                                                                            tGTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGCAAGAggg       <  2:767638/100‑1 (MQ=255)
                                                                                             gTAGTG‑TTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTCGTACTGCAAGAgggg      >  2:1909562/1‑100 (MQ=255)
                                                                                                  gtTTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGCAAGAGGGGGCCt  >  1:332195/1‑100 (MQ=255)
                                                                                                   |                                                                                                  
GTCCGCCAGAAAATCACCACGAATACCAGAATCGCGGCACTGACCAGAAAATGATAAACAGGAAACACGGGGCGGTTCACTTTGCTTTCTCCTGTAGTGTTTTCTGTAGGTTCTGAACCGGTTCTAGCGGGGTTGTGAGGCTGATGGCAATCGCCGGGCTCTTCCTGCATGTTACACTGGTACTGCAAGAGGGGGCCT  >  NC_000913/4500712‑4500909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A