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
A14 F129 I0 R1 205 159.3 7901478 93.8% 7411586 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 292,302 C→G 15.1% intergenic (+71/+20) yagJ → / ← yagK CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913292,3020CG15.1% 587.9 / 85.0 205intergenic (+71/+20)yagJ/yagKCP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein
Reads supporting (aligned to +/- strand):  ref base C (73/101);  new base G (14/17);  total (87/118)
Fisher's exact test for biased strand distribution p-value = 8.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

Only 100 of 207 total aligned reads displayed.

GTAGCGGACTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGTCC  >  NC_000913/292203‑292400
                                                                                                   |                                                                                                  
gtagCGGACTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCAc                                                                                                    >  1:1804404/1‑100 (MQ=255)
  agCGGACTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCAGTg                                                                                                  <  2:1412514/100‑1 (MQ=255)
  agCGGACTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTg                                                                                                  >  1:1085854/1‑100 (MQ=255)
  agCGGACTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTg                                                                                                  <  1:3333792/100‑1 (MQ=255)
     ggACTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTgaga                                                                                               <  2:1320874/100‑1 (MQ=255)
     ggACTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAAATGAATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTgaga                                                                                               >  1:375946/1‑100 (MQ=255)
       aCTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAg                                                                                             <  2:3736761/100‑1 (MQ=255)
       aCTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAg                                                                                             <  2:2485273/100‑1 (MQ=255)
        cTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAgg                                                                                            <  2:807694/100‑1 (MQ=255)
        cTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAgg                                                                                            <  2:359749/100‑1 (MQ=255)
         ttGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGc                                                                                           <  2:3123633/100‑1 (MQ=255)
          tGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCAGTGAGAAGGcc                                                                                          <  2:3009917/100‑1 (MQ=255)
          tGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGcc                                                                                          >  1:1537568/1‑100 (MQ=255)
          tGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGc                                                                                           >  1:3947894/1‑99 (MQ=255)
           gCTGATGACTATCAGTAATCTATAGATAATTGCGTAACTAAACTGCATTTTAGTAAATCTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCa                                                                                         <  2:2148010/100‑1 (MQ=255)
           gCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCAGTGAGAAGGcct                                                                                         <  1:95604/100‑2 (MQ=255)
           gCTGATGACTATCAGTAATCTATAGAAAAGTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCAGTGAGAAGGcct                                                                                         <  2:706941/100‑2 (MQ=255)
            ccaatgaCTATCAGTACTTTATATAAAATTGCGTAATTAAACTGCATTTTAGTAATTTTTTGAAACAATACACATAAGGCCTTCTCAGTGAGAAGGcct                                                                                         <  2:1762466/96‑2 (MQ=255)
             tgatgaCTATCAGTAATCTATAGAAAATTGCATAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCAGTGAGAAGGcctta                                                                                       <  2:660022/100‑4 (MQ=255)
              gatgaCTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCAGTGAGAAGGccttat                                                                                      <  1:1125604/100‑5 (MQ=255)
                  aCTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGa                                                                                  <  2:1667918/100‑1 (MQ=255)
                   cTATCAGTAATCTATAGAAAAGTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGAc                                                                                 <  2:3703130/100‑1 (MQ=255)
                    tATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACt                                                                                >  1:2613098/1‑100 (MQ=255)
                     aTCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACtt                                                                               >  1:132167/1‑100 (MQ=255)
                       cAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAGCAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTAc                                                                             <  1:2356164/100‑1 (MQ=255)
                       cAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTAc                                                                             <  1:3671134/100‑1 (MQ=255)
                       cAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTAc                                                                             <  1:2004031/100‑1 (MQ=255)
                       cAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTCAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTAc                                                                             >  1:553378/1‑100 (MQ=255)
                        aGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACa                                                                            >  1:127434/1‑100 (MQ=255)
                          tAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGt                                                                          <  1:2480152/100‑1 (MQ=255)
                           aaTCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGtt                                                                         >  1:1120254/1‑100 (MQ=255)
                           aaTCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGtt                                                                         >  1:3552821/1‑100 (MQ=255)
                              cTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGa                                                                      <  2:50800/100‑1 (MQ=255)
                                ataGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGAtt                                                                    >  1:3141490/1‑100 (MQ=255)
                                 taGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGAttt                                                                   <  1:3482621/100‑1 (MQ=255)
                                  aGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTTCAGTTCGATTTg                                                                  <  1:2602305/100‑1 (MQ=255)
                                  aGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTg                                                                  >  2:424845/1‑100 (MQ=255)
                                    aaaaTTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGc                                                                <  1:2647319/100‑1 (MQ=255)
                                       aTTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCt                                                               <  2:2865375/98‑1 (MQ=255)
                                         tGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAg                                                           <  1:2951476/100‑1 (MQ=255)
                                           cGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGcc                                                         <  1:2740512/100‑1 (MQ=255)
                                             tAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGa                                                       >  1:2538653/1‑100 (MQ=255)
                                              aaCGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGaa                                                      <  1:3387230/100‑1 (MQ=255)
                                              aaCGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGaa                                                      >  1:3611631/1‑100 (MQ=255)
                                               aCGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAg                                                     <  2:3786461/100‑1 (MQ=255)
                                                cGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGt                                                    >  1:3690026/1‑100 (MQ=255)
                                                     cTGCATTTTAGTAATTTTTTGAAACAATACAATTAAGGCCTTCTCACTGAGGAGGCCATTACCGACTTACAGTTCGATTTGGCTGCAGCCGAAGTTACgg                                               <  2:336089/100‑1 (MQ=255)
                                                     cTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACgg                                               <  2:3171518/100‑1 (MQ=255)
                                                     cTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACgg                                               <  2:1246135/100‑1 (MQ=255)
                                                     cTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACgg                                               <  2:2184926/100‑1 (MQ=255)
                                                      tGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGt                                              >  1:1178108/1‑100 (MQ=255)
                                                        cATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGtct                                            <  2:1619787/100‑1 (MQ=255)
                                                        cATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGtct                                            >  1:1381562/1‑100 (MQ=255)
                                                          ttttAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTcc                                          >  1:788513/1‑100 (MQ=255)
                                                          ttttAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTcc                                          >  1:1605194/1‑100 (MQ=255)
                                                           tttAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCt                                         <  2:2765729/100‑1 (MQ=255)
                                                             tAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTc                                       <  2:3552795/100‑1 (MQ=255)
                                                               gTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCAc                                     <  2:798304/100‑1 (MQ=255)
                                                                 aaTTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCa                                   <  1:3376495/100‑1 (MQ=255)
                                                                        tGAAACAATACAAATATGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACtt                            >  2:855992/1‑100 (MQ=255)
                                                                        tGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACtt                            >  1:447995/1‑100 (MQ=255)
                                                                          aaaCAATACAAATAAGGCCTTCTCACTGAGAATGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTg                          <  1:1463325/100‑1 (MQ=255)
                                                                          aaaCAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTg                          >  2:825714/1‑100 (MQ=255)
                                                                           aaCAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGc                         <  2:2688539/100‑1 (MQ=255)
                                                                             cAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCtt                       >  2:1089939/1‑100 (MQ=255)
                                                                               aTACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTc                     <  2:3947864/100‑1 (MQ=255)
                                                                                tACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCa                    <  1:1075927/100‑1 (MQ=255)
                                                                                tACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCa                    >  1:1970338/1‑100 (MQ=255)
                                                                                 aCAAAGAAGGCCTTCGCACTGTGTATGTCATGTCCGACGTACGATTACATTTGTCTTCAGCCGAAGTTACCGTCTCCTTCACCAAACACTTTGCTTTCa                    <  2:3205580/99‑1 (MQ=255)
                                                                                  cAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAAc                  >  1:2177262/1‑100 (MQ=255)
                                                                                  cAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAAc                  >  1:2975075/1‑100 (MQ=255)
                                                                                   ggtaatggCCTTCTCAGTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACt                 >  1:1480930/7‑100 (MQ=255)
                                                                                    aaTAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACtt                >  1:2462875/1‑100 (MQ=255)
                                                                                      aatggCCTTCTCAGTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTg              >  1:2911982/4‑100 (MQ=255)
                                                                                       atggCCTTCTCAGTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTg              >  1:869544/3‑99 (MQ=255)
                                                                                       aaGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTgg             <  2:87767/100‑1 (MQ=255)
                                                                                       aaGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTgg             <  2:4706/100‑1 (MQ=255)
                                                                                       aaGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTgg             <  1:3076766/100‑1 (MQ=255)
                                                                                        tggCCTTCTCAGTGAGAAGGCCATTACCGACTTGCAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTGTGCTTTCAACTTTGGt            >  2:2302078/2‑100 (MQ=255)
                                                                                        aGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGt            <  1:3785105/100‑1 (MQ=255)
                                                                                         ggCCTTCTCAGTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCTAACACTTTGCTTTCAACTTTGGTc           >  1:2855585/1‑100 (MQ=255)
                                                                                         ggCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTc           <  2:3396385/100‑1 (MQ=255)
                                                                                         ggCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTc           >  2:2993528/1‑100 (MQ=255)
                                                                                          gCCTTCTCAGTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCa          >  1:3272623/1‑100 (MQ=255)
                                                                                          gCCTTCTCAGTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCa          >  2:588533/1‑100 (MQ=255)
                                                                                          gCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCa          >  1:678978/1‑100 (MQ=255)
                                                                                           ccTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAg         <  2:1836658/100‑1 (MQ=255)
                                                                                           ccTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAg         >  1:3836416/1‑100 (MQ=255)
                                                                                            cTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAgg        >  1:3904701/1‑100 (MQ=255)
                                                                                             ttCTCACTGAGAAGGCCATTACCGACTTACGGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGt       <  1:480932/100‑1 (MQ=255)
                                                                                              tctcACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTa      <  2:127581/100‑1 (MQ=255)
                                                                                               ctcACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAg     >  1:3520805/1‑100 (MQ=255)
                                                                                                tcACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGt    >  2:3354179/1‑100 (MQ=255)
                                                                                                 cACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGTc   >  2:3858352/1‑100 (MQ=255)
                                                                                                 cACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGTc   >  1:1909124/1‑100 (MQ=255)
                                                                                                 cACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGTc   <  1:174294/100‑1 (MQ=255)
                                                                                                 cACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGTc   <  2:3685370/100‑1 (MQ=255)
                                                                                                  aCTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGTcc  <  1:2309556/100‑1 (MQ=255)
                                                                                                  aCTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGTcc  <  1:266537/100‑1 (MQ=255)
                                                                                                  aCTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTCTGGTCAGGTAGTcc  <  1:1440171/100‑1 (MQ=255)
                                                                                                   |                                                                                                  
GTAGCGGACTTGCTGATGACTATCAGTAATCTATAGAAAATTGCGTAACGAAACTGCATTTTAGTAATTTTTTGAAACAATACAAATAAGGCCTTCTCACTGAGAAGGCCATTACCGACTTACAGTTCGATTTGGCTACAGCCGAAGTTACGGTCTCCTTCACCAAACACTTTGCTTTCAACTTTGGTCAGGTAGTCC  >  NC_000913/292203‑292400

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