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 F142 I0 R1 175 91.2 4812830 94.5% 4548124 99.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,867,151 A→G 53.6% F134S (TTT→TCT)  rpoS ← RNA polymerase, sigma S (sigma 38) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,867,1510AG53.6% 33.2 / 151.3 117F134S (TTT→TCT) rpoSRNA polymerase, sigma S (sigma 38) factor
Reads supporting (aligned to +/- strand):  ref base A (26/28);  new base G (27/35);  total (54/63)
Fisher's exact test for biased strand distribution p-value = 7.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

Only 100 of 118 total aligned reads displayed.

AACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCAC  >  NC_000913/2867053‑2867248
                                                                                                  |                                                                                                 
 aCGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAAc                                                                                                 <  1:2019913/100‑1 (MQ=255)
  cGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACt                                                                                                <  2:114164/100‑1 (MQ=255)
      tAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTtctc                                                                                            <  2:2232992/100‑1 (MQ=255)
      tAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGGCAAACTtctc                                                                                            <  1:1273537/100‑1 (MQ=255)
      tAGTACGGGTTTGGGTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTtctc                                                                                            <  2:905515/100‑1 (MQ=255)
       aGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTctct                                                                                           <  1:296586/100‑1 (MQ=255)
       aGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTctct                                                                                           >  2:1032580/1‑100 (MQ=255)
       aGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTctct                                                                                           <  1:1693819/100‑1 (MQ=255)
        gTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTa                                                                                          >  1:1708238/1‑100 (MQ=255)
        gTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTa                                                                                          >  1:2335580/1‑100 (MQ=255)
        gTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGGCAAACTTCTCTa                                                                                          >  1:455008/1‑100 (MQ=255)
          aCGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTAcc                                                                                        <  2:327524/100‑1 (MQ=255)
             ggTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACcgtg                                                                                     <  1:1707481/100‑3 (MQ=255)
                   gTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATc                                                                               >  2:2302240/1‑100 (MQ=255)
                   gTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATc                                                                               >  1:1852988/1‑100 (MQ=255)
                   gTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATc                                                                               <  2:1548484/100‑1 (MQ=255)
                    ttCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCa                                                                              >  2:45307/1‑100 (MQ=255)
                    ttCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCa                                                                              >  1:994099/1‑100 (MQ=255)
                    ttCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCa                                                                              <  2:262216/100‑1 (MQ=255)
                      cATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGc                                                                            >  1:1171732/1‑100 (MQ=255)
                       aTAATCGCCCGTTCGATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGcc                                                                           <  1:1343812/100‑1 (MQ=255)
                       aTAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGcc                                                                           <  2:103553/100‑1 (MQ=255)
                          aTCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCa                                                                        <  1:719410/100‑1 (MQ=255)
                          aTCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCa                                                                        <  1:1866555/100‑1 (MQ=255)
                            cGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAgg                                                                      >  2:385371/1‑100 (MQ=255)
                              cccGTTCAATCGTCTGGCGAATCAACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGtt                                                                    >  2:1296184/1‑100 (MQ=255)
                                cGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGc                                                                  >  2:1774161/1‑100 (MQ=255)
                                cGTACAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGc                                                                  >  2:1027842/1‑100 (MQ=255)
                                 gTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGcc                                                                 <  2:655626/100‑1 (MQ=255)
                                  ttCAATCGTTTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGccc                                                                <  1:4681/100‑1 (MQ=255)
                                  ttCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGccc                                                                <  2:506203/100‑1 (MQ=255)
                                    cAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCctc                                                              >  1:2324901/1‑100 (MQ=255)
                                     aaTCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCctct                                                             <  1:2170442/100‑1 (MQ=255)
                                       tCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTc                                                           <  2:1181026/100‑1 (MQ=255)
                                       tCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTc                                                           <  1:359201/100‑1 (MQ=255)
                                       tCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTc                                                           <  2:2327113/100‑1 (MQ=255)
                                       tCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGATCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCATCTTc                                                           <  2:308148/100‑1 (MQ=255)
                                        cGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCg                                                          >  1:2029931/1‑100 (MQ=255)
                                         gTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGa                                                         <  1:1695530/100‑1 (MQ=255)
                                         gTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGa                                                         >  1:2378790/1‑100 (MQ=255)
                                          tCTGGCGAATCCACCAGGTTGCGTATGTTGAGCAGCGGACACAACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGAt                                                        <  2:1683433/100‑1 (MQ=255)
                                          tCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGAt                                                        >  1:1093570/1‑100 (MQ=255)
                                           cTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATa                                                       <  1:357461/100‑1 (MQ=255)
                                           cTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCACTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATa                                                       <  2:1472479/100‑1 (MQ=255)
                                            tagCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATaa                                                      >  1:1623821/3‑100 (MQ=255)
                                             tccgatctcaccaGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAg                                                     <  2:1819194/92‑1 (MQ=255)
                                             ggCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAg                                                     >  2:1294180/1‑100 (MQ=255)
                                             ggCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAg                                                     >  2:2185100/1‑100 (MQ=255)
                                             ggCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAg                                                     >  2:2128706/1‑100 (MQ=255)
                                                 aaTCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTcc                                                 >  1:2225186/1‑100 (MQ=255)
                                                  aTCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCa                                                <  1:2399048/100‑1 (MQ=255)
                                                  aTCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCa                                                <  1:2399015/100‑1 (MQ=255)
                                                  aTCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCa                                                >  2:1945429/1‑100 (MQ=255)
                                                  aTCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCa                                                >  1:2000322/1‑100 (MQ=255)
                                                    ccaccaGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGc                                              <  1:1948479/100‑1 (MQ=255)
                                                    ccaccaGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGGCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGc                                              >  2:432555/1‑100 (MQ=255)
                                                     caccaGGTTGCGTATGTTGAGAAGCGGAAACTACTTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTcc                                                 <  2:1191581/96‑1 (MQ=255)
                                                     caccaGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAgagatcgga                                             >  1:1819215/1‑92 (MQ=255)
                                                     caccaGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCa                                             <  2:1432598/100‑1 (MQ=255)
                                                      accaGGTTGCGTATGTTGAGAAGCGGAAACCTCGTTCCGGGTCATACTTCTCTACCGCGCGCATCAGCCGCAGGTTGCCCTCTTCGCTGAGGACCAGCaa                                            >  2:2379271/1‑100 (MQ=255)
                                                      accaGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGACAAGGTCCAGCaa                                            <  1:1571638/100‑1 (MQ=255)
                                                      accaGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGAAAAGGTCCAGCaa                                            <  1:1571826/100‑1 (MQ=255)
                                                          ggTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGcc                                        <  1:1121092/100‑1 (MQ=255)
                                                           gTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCa                                       <  1:1879360/100‑1 (MQ=255)
                                                             tGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAATCTTCTCTACCGCGCGGATCTGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGa                                     <  2:1304745/100‑1 (MQ=255)
                                                             tGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGGCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGa                                     >  1:41559/1‑100 (MQ=255)
                                                              gCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGAc                                    >  1:647784/1‑100 (MQ=255)
                                                              gCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGAc                                    <  1:109449/100‑1 (MQ=255)
                                                              gCGTATGTTGAGAAGCGGAAACCACGTTCCGGGGCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGAc                                    <  2:41558/100‑1 (MQ=255)
                                                               cGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGAcc                                   >  1:513466/1‑100 (MQ=255)
                                                               cGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGAcc                                   >  1:913581/1‑100 (MQ=255)
                                                               cGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGAcc                                   >  1:196987/1‑100 (MQ=255)
                                                                 tATGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCAc                                 >  1:1440603/1‑100 (MQ=255)
                                                                 tATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCAc                                 >  2:970564/1‑100 (MQ=255)
                                                                 tATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCAc                                 <  2:1823922/100‑1 (MQ=255)
                                                                 tATGTTGAGAAGCGGAAACCACGTTCCGGGGCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCAc                                 >  1:2037204/1‑100 (MQ=255)
                                                                   tGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGa                               >  1:88118/1‑100 (MQ=255)
                                                                   tGTTGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGa                               >  1:558245/1‑100 (MQ=255)
                                                                     ttGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGAtt                             >  1:1173016/1‑100 (MQ=255)
                                                                      tGAGAAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTg                            <  2:1041780/100‑1 (MQ=255)
                                                                       gagaAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAATGTCCAGCAACGCCAGACCACGATTGc                           >  1:474578/1‑100 (MQ=255)
                                                                       gagaAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGc                           >  2:1369795/1‑100 (MQ=255)
                                                                       gagaAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGc                           <  2:2049160/100‑1 (MQ=255)
                                                                       gagaAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGc                           <  1:731677/100‑1 (MQ=255)
                                                                        agaAGCTGAAACCACGTTCCGTGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGcc                          <  2:1803869/100‑1 (MQ=255)
                                                                        agaAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGcc                          <  2:88116/100‑1 (MQ=255)
                                                                        agaAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGcc                          <  1:1358421/100‑1 (MQ=255)
                                                                        agaAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGcc                          <  1:1897629/100‑1 (MQ=255)
                                                                         gaAGCGGAAACCACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCa                         <  1:1840860/100‑1 (MQ=255)
                                                                         gaAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGATCCAGCAACACAAGACCACGATAGCCa                         >  1:75553/1‑100 (MQ=255)
                                                                          aaGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCAt                        <  2:2335552/100‑1 (MQ=255)
                                                                              ggAAACCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAAcg                    >  1:851282/1‑100 (MQ=255)
                                                                                 aaCCACGTTCCGGGTCAAACTTCTCTACCGTGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAAcggcg                 >  2:1468766/1‑100 (MQ=255)
                                                                                   ccACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCggg               <  1:301126/100‑1 (MQ=255)
                                                                                    cACGTTCCGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGc              <  1:1870114/100‑1 (MQ=255)
                                                                                          ccGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAtttt        >  1:409451/1‑100 (MQ=255)
                                                                                           cGGGTCAGACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAttttt       <  1:1056636/100‑1 (MQ=255)
                                                                                           cGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAttttt       <  1:1996936/100‑1 (MQ=255)
                                                                                             ggTCAGACCTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCTACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTa      <  2:753817/99‑1 (MQ=255)
                                                                                                cAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTaccac  <  1:2203695/100‑1 (MQ=255)
                                                                                                  |                                                                                                 
AACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCAC  >  NC_000913/2867053‑2867248

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