Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I2 R1 1873 183.1 9376148 98.2% 9207377 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,106,978 A→G V210A (GTG→GCG)  rfbX ← putative O‑antigen transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,106,9780AG98.5% 394.1 / ‑2.4 129V210A (GTG→GCG) rfbXputative O‑antigen transporter
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (77/50);  total (78/51)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.01e-01

Only 100 of 133 total aligned reads displayed.

AATCCCAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGTCTGCTAAAGATCGACGCACATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACTT  >  NC_000913/2106888‑2107067
                                                                                          |                                                                                         
aaTCCCAGGATAATACCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGcgca                                                                                         <  1:2033720/93‑1 (MQ=255)
  acccAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCAtt                                                                                       <  2:1848591/92‑1 (MQ=255)
     cAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATg                                                                                    <  1:742102/93‑1 (MQ=255)
       ggATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTa                                                                                  <  2:1568440/93‑1 (MQ=255)
       ggATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTa                                                                                  <  2:4433959/93‑1 (MQ=255)
          taataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATg                                                                               >  2:130509/1‑93 (MQ=255)
           aataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGa                                                                              >  1:4500021/1‑93 (MQ=255)
           aataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGa                                                                              >  2:2001059/1‑93 (MQ=255)
           aataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGa                                                                              <  1:710490/93‑1 (MQ=255)
           aataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGa                                                                              <  1:1813508/93‑1 (MQ=255)
           aataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGa                                                                              <  2:1565436/93‑1 (MQ=255)
           aataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGa                                                                              <  1:2870861/93‑1 (MQ=255)
            ataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGAt                                                                             >  1:2635852/1‑93 (MQ=255)
            ataaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGAt                                                                             >  1:1914728/1‑93 (MQ=255)
             taaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAATATCGACGCGCATTATGTAATGATa                                                                            >  2:4539698/1‑93 (MQ=255)
             taaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATa                                                                            <  1:185119/93‑1 (MQ=255)
             taaCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATa                                                                            <  2:3923437/93‑1 (MQ=255)
              aaCTATTCCCGTGGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAg                                                                           >  1:528614/1‑93 (MQ=255)
               aCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGc                                                                          >  1:2226479/1‑93 (MQ=255)
                cTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCg                                                                         >  2:526408/1‑93 (MQ=255)
                cTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCg                                                                         >  2:2808981/1‑93 (MQ=255)
                 tATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGt                                                                        >  1:2381095/1‑93 (MQ=255)
                  aTTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTa                                                                       >  2:2624619/1‑93 (MQ=255)
                     cccGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACt                                                                    <  2:2617016/93‑1 (MQ=255)
                     cccGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACt                                                                    >  1:3906053/1‑93 (MQ=255)
                     cccGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACt                                                                    <  2:2317930/93‑1 (MQ=255)
                      ccGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACtt                                                                   >  1:588377/1‑93 (MQ=255)
                            aaTATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCaa                                                             >  2:854349/1‑93 (MQ=255)
                            aaTATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCaa                                                             >  2:2826448/1‑93 (MQ=255)
                             atatAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAAt                                                            <  2:3421384/93‑1 (MQ=255)
                             atatAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAAt                                                            <  1:3480153/93‑1 (MQ=255)
                              tataAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATc                                                           >  1:2038745/1‑93 (MQ=255)
                               ataAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATcc                                                          >  2:2320193/1‑93 (MQ=255)
                               ataAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATcc                                                          <  2:2637341/93‑1 (MQ=255)
                                taAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCa                                                         <  1:1644025/93‑1 (MQ=255)
                                taAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCa                                                         >  1:1901619/1‑93 (MQ=255)
                                taAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCa                                                         >  1:2588574/1‑93 (MQ=255)
                                  aaCTAATAGCAGATGTGGCAATAAAAACATGAAAACCGCCTGCTCAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAAc                                                       >  2:707954/1‑93 (MQ=255)
                                    cTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCt                                                     <  2:4310940/93‑1 (MQ=255)
                                     tAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCtt                                                    >  2:1209759/1‑93 (MQ=255)
                                     tAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCtt                                                    >  2:634151/1‑93 (MQ=255)
                                     tAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCtt                                                    >  2:2718553/1‑93 (MQ=255)
                                     tAATAGCAGATGTGGAAATAAAAACATGAAAACCACCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCtt                                                    >  2:4042853/1‑93 (MQ=255)
                                       aTAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCa                                                  <  1:2988887/93‑1 (MQ=255)
                                         aGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATg                                                >  2:3599834/1‑93 (MQ=255)
                                          gCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGa                                               >  1:3444889/1‑93 (MQ=255)
                                           cAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaa                                              <  2:3212479/93‑1 (MQ=255)
                                           cAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaa                                              <  1:1572443/93‑1 (MQ=255)
                                            aGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaac                                             >  2:1580096/1‑93 (MQ=255)
                                            aGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaac                                             <  2:954730/93‑1 (MQ=255)
                                             gATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaaca                                            >  1:1315150/1‑93 (MQ=255)
                                             gATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaaca                                            >  1:2660029/1‑93 (MQ=255)
                                             gATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaaca                                            >  1:4304209/1‑93 (MQ=255)
                                              aTGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaacaa                                           <  1:835393/93‑1 (MQ=255)
                                              aTGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaacaa                                           <  1:3155749/93‑1 (MQ=255)
                                              aTGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaacaa                                           <  1:4551270/93‑1 (MQ=255)
                                               tgtgGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAATCTTCATGaacaac                                          >  2:3028899/1‑93 (MQ=255)
                                               tgtgGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaacaac                                          >  2:1163295/1‑93 (MQ=255)
                                               tgtgGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGaacaac                                          >  1:3556135/1‑93 (MQ=255)
                                                  ggAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGAt                                       <  2:1829571/93‑1 (MQ=255)
                                                  ggAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGAt                                       <  1:2330033/93‑1 (MQ=255)
                                                  ggAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGAt                                       <  1:2647455/93‑1 (MQ=255)
                                                   gAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATa                                      <  2:3656064/93‑1 (MQ=255)
                                                     aaTAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGc                                    >  2:3672294/1‑93 (MQ=255)
                                                     aaTAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGc                                    >  1:308977/1‑93 (MQ=255)
                                                       aaaaaaCATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTa                                  <  2:3319436/92‑1 (MQ=255)
                                                        aaaaaCATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAg                                 >  1:2350715/1‑93 (MQ=255)
                                                         aaaaCATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGt                                >  1:2751081/1‑93 (MQ=255)
                                                         aaaaCATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGt                                >  2:3631466/1‑93 (MQ=255)
                                                          aaaCATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTg                               >  2:1327983/1‑93 (MQ=255)
                                                            aCATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCa                             >  1:4290687/1‑93 (MQ=255)
                                                             cATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCaa                            >  1:4413636/1‑93 (MQ=255)
                                                             cATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCaa                            >  1:1418110/1‑93 (MQ=255)
                                                              aTGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCaat                           >  1:1268232/1‑93 (MQ=255)
                                                               tGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCaata                          >  2:2435888/1‑93 (MQ=255)
                                                                 aaaaCCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCaataat                        <  2:3378531/93‑1 (MQ=255)
                                                                   aaCCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTc                      <  2:3072561/93‑1 (MQ=255)
                                                                   aaCCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTc                      >  2:2416528/1‑93 (MQ=255)
                                                                    aCCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTcc                     >  1:4556642/1‑93 (MQ=255)
                                                                       gccTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGc                  >  2:4318901/3‑93 (MQ=255)
                                                                       gccTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGc                  <  1:4366030/91‑1 (MQ=255)
                                                                       gccTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGc                  >  2:3783609/3‑93 (MQ=255)
                                                                        ccTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCa                 <  1:4617066/92‑1 (MQ=255)
                                                                         cTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCaa                >  2:4105256/1‑93 (MQ=255)
                                                                          tGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAAc               <  1:3758885/93‑1 (MQ=255)
                                                                          tGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAAc               <  2:1121474/93‑1 (MQ=255)
                                                                            cTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCa             <  2:1956144/93‑1 (MQ=255)
                                                                             tAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAg            >  2:947018/1‑93 (MQ=255)
                                                                              aaaGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGa           <  2:4459874/93‑1 (MQ=255)
                                                                              aaaGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGa           <  2:4235662/93‑1 (MQ=255)
                                                                               aaGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGAt          >  1:1105041/1‑93 (MQ=255)
                                                                               aaGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGAt          <  1:4429685/93‑1 (MQ=255)
                                                                                 gATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCCACCAGAttt        >  2:1141303/1‑93 (MQ=255)
                                                                                 gATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGAttt        >  1:3832655/1‑93 (MQ=255)
                                                                                  aTCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTg       >  2:3724935/1‑93 (MQ=255)
                                                                                   tCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGc      >  1:4224062/1‑93 (MQ=255)
                                                                                    cGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCa     <  1:1706380/93‑1 (MQ=255)
                                                                                    cGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCa     <  1:1433541/93‑1 (MQ=255)
                                                                                       cgcgCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACtt  >  1:1750232/1‑93 (MQ=255)
                                                                                       cgcgCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACtt  >  2:2442242/1‑93 (MQ=255)
                                                                                          |                                                                                         
AATCCCAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGTCTGCTAAAGATCGACGCACATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACTT  >  NC_000913/2106888‑2107067

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ATAAATCCCAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGTCTGCTAAAGATCGACGCACATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACTTGACT  >  NC_000913/2106885‑2107071
                                                                                             |                                                                                             
ATAAATCCCAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCG                                                                                               >  SRR4302535.905099/1‑94 (MQ=60)
 TAAATCCCAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGC                                                                                              >  SRR4302535.4027461/1‑94 (MQ=60)
  AAATCCCAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCA                                                                                             <  SRR4302535.437831/94‑1 (MQ=60)
   AATCCCAGGATAATACCTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCAT                                                                                            <  SRR4302535.2048373/94‑1 (MQ=60)
        CAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGT                                                                                       <  SRR4302535.747315/94‑1 (MQ=60)
         AGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTA                                                                                      >  SRR4302535.4502067/1‑94 (MQ=60)
           GATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAAT                                                                                    >  SRR4302535.1972919/1‑94 (MQ=60)
             TAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGA                                                                                  >  SRR4302535.4530927/1‑94 (MQ=60)
              AATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGAT                                                                                 >  SRR4302535.2654737/1‑94 (MQ=60)
              AATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGAT                                                                                 <  SRR4302535.2891201/94‑1 (MQ=60)
              AATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGAT                                                                                 >  SRR4302535.1928526/1‑94 (MQ=60)
              AATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGAT                                                                                 <  SRR4302535.1826622/94‑1 (MQ=60)
              AATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGAT                                                                                 <  SRR4302535.715476/94‑1 (MQ=60)
                TAACTATTCCCGTGGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAG                                                                               >  SRR4302535.532308/1‑94 (MQ=60)
                TAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAG                                                                               <  SRR4302535.186395/94‑1 (MQ=60)
                 AACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGC                                                                              >  SRR4302535.2242320/1‑94 (MQ=60)
                  ACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCG                                                                             >  SRR4302535.1667754/1‑94 (MQ=60)
                   CTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGT                                                                            >  SRR4302535.2398194/1‑94 (MQ=60)
                       TCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACT                                                                        >  SRR4302535.3932815/1‑94 (MQ=60)
                        CCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTT                                                                       >  SRR4302535.592503/1‑94 (MQ=60)
                                ATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATC                                                               >  SRR4302535.2053425/1‑94 (MQ=60)
                                ATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATC                                                               <  SRR4302535.3504330/94‑1 (MQ=60)
                                  ATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCA                                                             >  SRR4302535.1915307/1‑94 (MQ=60)
                                  ATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCA                                                             >  SRR4302535.2607164/1‑94 (MQ=60)
                                   TAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAA                                                            <  SRR4302535.1655909/94‑1 (MQ=60)
                                       CTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTT                                                        >  SRR4302535.2267145/1‑94 (MQ=60)
                                       CTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTT                                                        >  SRR4302535.4338741/1‑94 (MQ=60)
                                       CTAATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTT                                                        <  SRR4302535.1856368/94‑1 (MQ=60)
                                          ATAGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCAT                                                     <  SRR4302535.3009842/94‑1 (MQ=60)
                                            AGCAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGA                                                   >  SRR4302535.3468843/1‑94 (MQ=60)
                                              CAGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAAC                                                 <  SRR4302535.1583793/94‑1 (MQ=60)
                                               AGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACA                                                >  SRR4302535.2679085/1‑94 (MQ=60)
                                               AGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACA                                                >  SRR4302535.4333657/1‑94 (MQ=60)
                                               AGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACA                                                >  SRR4302535.1324546/1‑94 (MQ=60)
                                               AGATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGAAATGATAGCGTAACTTTACCCATCCAACCTTCATGAACA                                                >  SRR4302535.2679083/1‑94 (MQ=60)
                                                 ATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAAC                                              <  SRR4302535.841252/94‑1 (MQ=60)
                                                 ATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAAC                                              <  SRR4302535.4582375/94‑1 (MQ=60)
                                                 ATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAAC                                              <  SRR4302535.3177666/94‑1 (MQ=60)
                                                 ATGTGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAAC                                              >  SRR4302535.3580800/1‑94 (MQ=60)
                                                    TGGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGAT                                           >  SRR4302535.409798/1‑94 (MQ=60)
                                                     GGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATA                                          <  SRR4302535.2346699/94‑1 (MQ=60)
                                                     GGAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATA                                          <  SRR4302535.2666419/94‑1 (MQ=60)
                                                      GAAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAG                                         <  SRR4302535.2494935/94‑1 (MQ=60)
                                                       AAATAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGC                                        >  SRR4302535.311120/1‑94 (MQ=60)
                                                          TAAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAG                                     >  SRR4302535.2367569/1‑94 (MQ=60)
                                                           AAAAACATGAAAACCGTCTGCTAAAGATCGACGCACATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGT                                    <  SRR4302535.3246210/94‑1 (MQ=60)
                                                           AAAAACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGT                                    >  SRR4302535.2770692/1‑94 (MQ=60)
                                                              AACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCA                                 >  SRR4302535.4320034/1‑94 (MQ=60)
                                                               ACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAA                                >  SRR4302535.4443843/1‑94 (MQ=60)
                                                               ACATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAA                                >  SRR4302535.1428234/1‑94 (MQ=60)
                                                                CATGAAAACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAAT                               >  SRR4302535.1277303/1‑94 (MQ=60)
                                                                      AACCGCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCC                         >  SRR4302535.4587758/1‑94 (MQ=60)
                                                                          GCCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCA                     <  SRR4302535.4395903/94‑1 (MQ=60)
                                                                           CCTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAA                    <  SRR4302535.4648442/94‑1 (MQ=60)
                                                                            CTGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAAC                   >  SRR4302535.1428255/1‑94 (MQ=60)
                                                                             TGCTAAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACC                  <  SRR4302535.3784871/94‑1 (MQ=60)
                                                                                 AAAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGAT              >  SRR4302535.1112937/1‑94 (MQ=60)
                                                                                 AAAGATCGACGCGCATTATGT‑ATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATT             <  SRR4302535.863299/94‑1 (MQ=60)
                                                                                  AAGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATT             <  SRR4302535.4460035/94‑1 (MQ=60)
                                                                                   AGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTT            >  SRR4302535.3859085/1‑94 (MQ=60)
                                                                                   AGATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTT            <  SRR4302535.683983/94‑1 (MQ=60)
                                                                                    GATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTG           >  SRR4302535.2903934/1‑94 (MQ=60)
                                                                                     ATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGC          >  SRR4302535.373325/1‑94 (MQ=60)
                                                                                     ATCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGC          >  SRR4302535.4252965/1‑94 (MQ=60)
                                                                                      TCGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATCAACATCGTTAGCTAGTGCAATAATTCCAGCAACCAGATTTACA         <  SRR4302535.1380535/94‑1 (MQ=60)
                                                                                       CGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCAC        <  SRR4302535.1443777/94‑1 (MQ=60)
                                                                                       CGACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCAC        <  SRR4302535.1718714/94‑1 (MQ=60)
                                                                                         ACGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACTT      >  SRR4302535.1762890/1‑94 (MQ=60)
                                                                                          CGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACTTG     <  SRR4302535.4617498/94‑1 (MQ=60)
                                                                                          CGCGCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACTTG     >  SRR4302535.1658244/1‑94 (MQ=60)
                                                                                             GCATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACNANGATAGCTAGTGCAATAATTCCAGCAACCAGATTNGCACTTGACT  <  SRR4302535.4267211/94‑1 (MQ=60)
                                                                                             |                                                                                             
ATAAATCCCAGGATAATAACTATTCCCGTAGAATATAAACTAATAGCAGATGTGGAAATAAAAACATGAAAACCGTCTGCTAAAGATCGACGCACATTATGTAATGATAGCGTAACTTTACCAATCCAACCTTCATGAACAACGATAGCTAGTGCAATAATTCCAGCAACCAGATTTGCACTTGACT  >  NC_000913/2106885‑2107071

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑