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
A12 F133 I0 R1 200 171.4 8351354 94.3% 7875326 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,652,242 T→G 83.0% pseudogene (692/1158 nt) intQ → pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,652,2420TG83.0% 314.1 / 46.2 122pseudogene (692/1158 nt)intQpseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base T (8/13);  new base G (58/43);  total (66/56)
Fisher's exact test for biased strand distribution p-value = 1.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

Only 100 of 141 total aligned reads displayed.

GGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCAGAGA  >  NC_000913/1652143‑1652338
                                                                                                   |                                                                                                
gggAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGt                                                                                                  <  1:2878265/100‑1 (MQ=255)
gggAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGt                                                                                                  <  2:3992950/100‑1 (MQ=255)
 ggaggaCATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGtc                                                                                                 >  1:3918516/1‑100 (MQ=255)
   aggaCATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGtcat                                                                                               >  2:2099334/1‑100 (MQ=255)
   aggaCATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGgcat                                                                                               <  2:472646/100‑1 (MQ=255)
    ggaCATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGgcatt                                                                                              >  1:1032239/1‑100 (MQ=255)
      aCATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGgcattca                                                                                            <  1:661202/100‑1 (MQ=255)
      aCATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGgcattca                                                                                            <  1:1034638/100‑1 (MQ=255)
       cATAGATCTGAAAAATGGAACAATGATGCTCAGGAGAAATTTAGCAAAAGACAGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGgaattca                                                                                            >  2:1763354/1‑99 (MQ=255)
       cATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGtcattcat                                                                                           >  1:1898409/1‑100 (MQ=255)
       cATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGgcattcat                                                                                           >  2:56766/1‑100 (MQ=255)
        aTAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGgcattca                                                                                            <  1:1891482/98‑1 (MQ=255)
        aTAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATc                                                                                          <  1:2626900/100‑1 (MQ=255)
        aTAAATCTAAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATc                                                                                          <  2:22627/100‑1 (MQ=255)
         tAGATCTGCAAAATGGAACAATGATGATCAGAAAAAATTTAACAAAAGATCGATTAAAGAAAACAAAAAAATAGACGTGAATCAATAGGTtcattc                                                                                             >  2:783709/1‑96 (MQ=255)
         tAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCt                                                                                         >  1:1917360/1‑100 (MQ=255)
         tAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCt                                                                                         <  1:3360927/100‑1 (MQ=255)
         naGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCt                                                                                         >  1:688523/2‑100 (MQ=255)
           gATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCtta                                                                                       >  2:4009474/1‑100 (MQ=255)
            aTCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCttat                                                                                      >  2:3083913/1‑100 (MQ=255)
            aTCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCttan                                                                                      <  1:1495096/100‑2 (MQ=255)
            aTCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAAAACAGGCGGGAACCAATCGGGGCATTCATCttat                                                                                      <  2:926591/100‑1 (MQ=255)
             tCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCttatt                                                                                     >  1:4043171/1‑100 (MQ=255)
             tCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCttatt                                                                                     >  2:1217282/1‑100 (MQ=255)
             tCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCttatt                                                                                     >  1:988176/1‑100 (MQ=255)
             tCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACC‑AAAACACAGGCGGGAACCAATCGGGGCATTCATCttatta                                                                                    >  1:311740/1‑100 (MQ=255)
              ntGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAGGACCGTTTCACGGTACCAATAACACAGGCGGGAACCAATCGGGTCATTCATCttatta                                                                                    >  2:2268919/2‑100 (MQ=255)
              cTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCttatta                                                                                    <  1:1900752/100‑1 (MQ=255)
              cTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCttatta                                                                                    >  1:1947224/1‑100 (MQ=255)
               tGAGAAATGGAACAATGATGATGAGGAGAAATTGAACAAAAAACCGTTTTACGTTATCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCttat                                                                                      <  2:1100583/97‑1 (MQ=255)
                gAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAg                                                                                  >  1:1871206/1‑100 (MQ=255)
                  aaaaTGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGcc                                                                                >  1:4026835/1‑100 (MQ=255)
                  aaaaTGGAACAATGATGATCAGGAAAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGcc                                                                                <  2:1396396/100‑1 (MQ=255)
                   aaaTGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCa                                                                               >  2:2948685/1‑100 (MQ=255)
                    aaTGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCACTCGGGGCATTCATCTTATTAAGCCAg                                                                              >  2:2667825/1‑100 (MQ=255)
                    aaTGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAg                                                                              <  1:1937604/100‑1 (MQ=255)
                       ggAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCaa                                                                           >  2:4093472/1‑100 (MQ=255)
                        gAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAAt                                                                          <  1:3332078/100‑1 (MQ=255)
                         aaCACTGAGGATCAGGACAAATTTAGCAAGAGACAGATTCACGGTACCAAAAACACACGCGGTAACCCTTTGGGGCATTGATCTTATTAATCCAGCACTc                                                                         >  2:1135864/1‑100 (MQ=255)
                         aaCAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATc                                                                         <  2:3425623/100‑1 (MQ=255)
                          aCAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACATGCGGGAACCAATCTGGGCATTCATCTTATTAAGCCAGCAATCg                                                                        >  2:1025950/1‑100 (MQ=255)
                           cAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGAGCATTCATCTTATTAAGCCAGCAATcaa                                                                       >  2:2523270/1‑98 (MQ=255)
                            aaTGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGAc                                                                      <  1:2362041/100‑1 (MQ=255)
                              tgatgaTCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGc                                                                    >  2:3652635/1‑100 (MQ=255)
                                 tgatCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGctct                                                                 >  1:1250698/1‑100 (MQ=255)
                                 tgatCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGctct                                                                 >  2:321927/1‑100 (MQ=255)
                                  gatCAGGAGAAATTTAGCAAAATACCGTTTCACGGTACCAAAAACACCGGCGGGAACCAATCGTGGCTTTCACCTTATTAAGCCAGCATTCGACGctc                                                                  >  2:3490024/1‑98 (MQ=255)
                                  gatCAGGAGAAATTTAGCAAAAGACCGTTTCACTGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCtctc                                                                <  2:1411253/100‑1 (MQ=255)
                                   atCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTcc                                                               >  2:2503815/1‑100 (MQ=255)
                                      aGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGa                                                            >  1:764363/1‑100 (MQ=255)
                                       ggAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAg                                                           <  2:1897352/100‑1 (MQ=255)
                                       ggAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAg                                                           >  2:396653/1‑100 (MQ=255)
                                       ggAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAg                                                           <  1:1027700/100‑1 (MQ=255)
                                       ggAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAg                                                           <  1:181761/100‑1 (MQ=255)
                                        gagaAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGt                                                          <  1:4147839/100‑1 (MQ=255)
                                         agaAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTc                                                         >  2:1779592/1‑100 (MQ=255)
                                           aaaTTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAg                                                       <  2:3301715/100‑1 (MQ=255)
                                             aTTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGAt                                                     <  1:1755306/100‑1 (MQ=255)
                                              tttAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATg                                                    <  1:3245668/100‑1 (MQ=255)
                                                 aGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACa                                                 >  1:537266/1‑100 (MQ=255)
                                                  gCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACAt                                                >  1:864903/1‑100 (MQ=255)
                                                   cAAAAAGCCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGAc                                                  <  2:2571064/97‑1 (MQ=255)
                                                       aGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACg                                           <  1:3724602/100‑1 (MQ=255)
                                                          ccGTTTCACGGTACCAAAAACACAGGCCGGAACCAATCGGGGCATTCATCTTATTAAGCCAGTAATCGACGCTCTCCGGAGTCAGATGACATTAACga                                          <  2:3564124/98‑1 (MQ=255)
                                                           cGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGAc                                       <  1:2760979/100‑1 (MQ=255)
                                                           cGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGAc                                       <  2:134805/100‑1 (MQ=255)
                                                              ttCATGGTACCAAAAACACAGGCGGGTACCAATCGGGGCATTCATCATCTTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACAATAACGAGCCTGa                                    >  2:2386961/1‑100 (MQ=255)
                                                               tCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAg                                   <  1:972852/100‑1 (MQ=255)
                                                                cACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGc                                  >  1:2067456/1‑100 (MQ=255)
                                                                cACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGc                                  >  1:387079/1‑100 (MQ=255)
                                                                cACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTACGGAGACAGATGAGATTAACGGGACTgcg                                   >  1:3469075/1‑97 (MQ=255)
                                                                 aCGGTACGAAAAACACAGGCGGGAACCAATCGGGGCATTCAGCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCa                                 <  2:3312541/100‑1 (MQ=255)
                                                                 aCGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCa                                 <  1:698692/100‑1 (MQ=255)
                                                                   ggTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCaaa                               <  2:1917350/100‑1 (MQ=255)
                                                                     tACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGGCTGAGCAAaga                             <  2:1757880/100‑1 (MQ=255)
                                                                      aCCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGCCACTGAGCaacgcg                            >  1:2424651/1‑96 (MQ=255)
                                                                      aCCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAagag                            <  1:2583508/100‑1 (MQ=255)
                                                                       ccAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGc                           >  1:1039045/1‑100 (MQ=255)
                                                                       ccAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGGCAGATGACATTAACGAGACTGAGCAAAGAGc                           >  2:46447/1‑100 (MQ=255)
                                                                        cAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCa                          >  1:4047182/1‑100 (MQ=255)
                                                                        cAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCa                          >  1:3594240/1‑100 (MQ=255)
                                                                        cAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCa                          >  2:3743189/1‑100 (MQ=255)
                                                                         aaaaaCACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCat                         >  1:3067552/1‑100 (MQ=255)
                                                                         aaaaaCACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGCCAGATGACATGAACGAGACCGAGCAAAGAGc                           >  2:9400/1‑98 (MQ=255)
                                                                          aaaaCACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCata                        <  1:210798/100‑1 (MQ=255)
                                                                           aaaCACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCatat                       <  2:298218/100‑1 (MQ=255)
                                                                                caGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATAACATTAACGAGACTGAGCAAAGAGCATATCATTg                  >  2:536565/1‑100 (MQ=255)
                                                                                  ggCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGAt                <  1:778528/100‑1 (MQ=255)
                                                                                   gcaggAACCAATCGTGTCATTCATCTTATTAATCCAGCAATCTACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATg               <  2:2724075/97‑1 (MQ=255)
                                                                                   gCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATg               <  1:702833/100‑1 (MQ=255)
                                                                                   gCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATg               <  1:3128394/100‑1 (MQ=255)
                                                                                       gAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCa           <  1:172294/100‑1 (MQ=255)
                                                                                        aaCCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCAc          >  2:2059839/1‑100 (MQ=255)
                                                                                            aaTCGGGGCATTCATGGTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACCTTAACGAGACTGAGCACAAAGCATATCAGTGATGTTCACTTCa      >  2:4074198/1‑100 (MQ=255)
                                                                                            aaTCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCa      >  1:1254390/1‑100 (MQ=255)
                                                                                            aaTCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCa      >  1:1081694/1‑100 (MQ=255)
                                                                                             aTCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCag     <  2:1311514/100‑1 (MQ=255)
                                                                                              tCGGGGCATTCATCTTATTAAGCCAGCAATCGACGACCTCCGGAGTCAGATGACATTAGCGAGACTGAGCAAAGAGCTTATCATTGAGGTTCACTTgaga    <  2:2424636/100‑1 (MQ=255)
                                                                                                ggggCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCcgaga  >  2:2340499/1‑100 (MQ=255)
                                                                                                ggggCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCagaga  >  2:3016720/1‑100 (MQ=255)
                                                                                                   |                                                                                                
GGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCAGAGA  >  NC_000913/1652143‑1652338

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A