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 I1 R1 1357 179.3 9500450 96.1% 9129932 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,962,105 C→T A324T (GCC→ACC)  flhA ← FlhA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,962,1050CT99.1% 377.4 / ‑5.1 111A324T (GCC→ACC) flhAFlhA
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (49/61);  total (50/61)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.55e-01

Only 100 of 118 total aligned reads displayed.

ACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCTT  >  NC_000913/1962015‑1962193
                                                                                          |                                                                                        
aCGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCa                                                                                        >  1:894598/1‑93 (MQ=255)
 cGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAg                                                                                       >  1:448144/1‑93 (MQ=255)
  gTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGc                                                                                      >  2:2298819/1‑93 (MQ=255)
   tCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGcc                                                                                     >  1:2694544/1‑93 (MQ=255)
     gCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCg                                                                                   >  1:1637074/1‑93 (MQ=255)
     gCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCg                                                                                   >  1:2059630/1‑93 (MQ=255)
     gCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCg                                                                                   <  1:4476622/93‑1 (MQ=255)
      cTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTGAGCCCGa                                                                                  >  2:1023847/1‑93 (MQ=255)
      cTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGa                                                                                  <  2:3094384/93‑1 (MQ=255)
       ttCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAg                                                                                 >  1:440192/1‑93 (MQ=255)
         cGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTTAGCCCGAGCa                                                                               >  2:3794642/1‑93 (MQ=255)
           aCAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAAt                                                                             >  1:35433/1‑93 (MQ=255)
           aCAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCATATCCACCAGGTCAGCCCGAGCaac                                                                             >  1:957488/1‑92 (MQ=255)
             aaCGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCCGGTCAGCCCGAGCAATcc                                                                           >  1:4083991/1‑93 (MQ=255)
             aaCGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATcc                                                                           >  1:661895/1‑93 (MQ=255)
               cGGTATTATTCTCTGCCGAATTTAACGGTTTGGATTCGGCTGGCGATTTTTGTTCGCGTCAGCGTATCCACCAAGTCAGCCCGAGCAATccag                                                                         <  1:4221452/93‑3 (MQ=255)
               cGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCgg                                                                         <  2:2903234/93‑1 (MQ=255)
                ggTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGc                                                                        <  2:1212544/93‑1 (MQ=255)
                ggTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGc                                                                        <  1:1234366/93‑1 (MQ=255)
                cgTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGc                                                                        <  1:3140638/92‑1 (MQ=255)
                 gTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCa                                                                       >  2:4282449/1‑93 (MQ=255)
                  tattatTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAg                                                                      <  1:4613730/93‑1 (MQ=255)
                   attattCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGGCATCCGGCAGt                                                                     >  2:3501370/1‑93 (MQ=255)
                    ttattCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTg                                                                    >  2:4726627/1‑93 (MQ=255)
                     tattCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGGTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCACGCAGTGa                                                                   >  1:4046547/1‑93 (MQ=255)
                     tattCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGa                                                                   >  1:4046548/1‑93 (MQ=255)
                       ttCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAAc                                                                 >  1:1354504/1‑93 (MQ=255)
                         ctctTCCAATTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAg                                                               <  2:3599474/93‑1 (MQ=255)
                         ctctGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAg                                                               <  2:3599473/93‑1 (MQ=255)
                         ctctGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAg                                                               >  2:1272598/1‑93 (MQ=255)
                          tctGCCATTTTTTCCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGc                                                              <  2:3551049/93‑1 (MQ=255)
                            tGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaa                                                            >  2:1692543/1‑93 (MQ=255)
                            tGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaa                                                            >  2:3821523/1‑93 (MQ=255)
                              ccATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaaaa                                                          >  1:4394876/1‑93 (MQ=255)
                              ccATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaaaa                                                          >  1:102800/1‑93 (MQ=255)
                              ccATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaaaa                                                          >  1:4064495/1‑93 (MQ=255)
                              ccATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCaaaa                                                          >  1:4042066/1‑93 (MQ=255)
                               cATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaaaaa                                                         <  1:1857700/93‑1 (MQ=255)
                               cATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaaaaa                                                         >  1:71837/1‑93 (MQ=255)
                                aTTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAAt                                                        >  1:3838375/1‑93 (MQ=255)
                                aTTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAAt                                                        >  1:2780846/1‑93 (MQ=255)
                                 tttttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATa                                                       <  1:4064282/93‑1 (MQ=255)
                                 tttttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATa                                                       >  2:2267989/1‑93 (MQ=255)
                                   tttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCCGGTCAGCCCGAGCAATCCGGCAGTGAACCGCAAAAATAcc                                                     >  1:2095180/1‑93 (MQ=255)
                                   tttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATAcc                                                     <  2:4003172/93‑1 (MQ=255)
                                    ttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCa                                                    <  1:449626/93‑1 (MQ=255)
                                     tACCGGTTTGGGTTCGGGTGGCGCTTTTTGTTCGCGTCCGCGTATTCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATAACAg                                                   >  1:2175918/1‑93 (MQ=255)
                                     tACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAg                                                   <  2:665914/93‑1 (MQ=255)
                                     tACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAg                                                   <  2:3099753/93‑1 (MQ=255)
                                      aCCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAgg                                                  <  1:870475/93‑1 (MQ=255)
                                       ccGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGt                                                 >  1:2264251/1‑93 (MQ=255)
                                         ggTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTc                                               <  2:3868502/93‑1 (MQ=255)
                                         ggTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTc                                               <  1:3579622/93‑1 (MQ=255)
                                          gTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCg                                              <  2:2282960/93‑1 (MQ=255)
                                           tttGGGTTCGGCTGGCGCTTTTTTTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCACGTTCgg                                             <  2:4606691/93‑1 (MQ=255)
                                            ttGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGc                                            >  2:1640265/1‑93 (MQ=255)
                                              gggTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCAt                                          <  2:4483329/93‑1 (MQ=255)
                                              gggTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCAt                                          <  1:1113528/93‑1 (MQ=255)
                                              gggTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCAt                                          <  1:3933007/93‑1 (MQ=255)
                                               ggTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCAtt                                         >  1:1965433/1‑93 (MQ=255)
                                                gTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTc                                        <  1:939960/93‑1 (MQ=255)
                                                 ttCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTcc                                       <  2:4130995/93‑1 (MQ=255)
                                                   cGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAg                                     <  1:1644786/93‑1 (MQ=255)
                                                      ctggCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCa                                  <  1:4180969/91‑1 (MQ=255)
                                                      ctggCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCa                                  <  1:1229051/91‑1 (MQ=255)
                                                       tggCGCTTTTTGTTCGCGTCCGCGTGTCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCAc                                 >  2:139287/2‑93 (MQ=255)
                                                         gcgcTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCa                               <  2:48496/93‑1 (MQ=255)
                                                         gcgcTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCa                               >  1:3432740/1‑93 (MQ=255)
                                                          cgcTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAg                              <  2:107698/93‑1 (MQ=255)
                                                          cgcTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAg                              <  1:1534832/93‑1 (MQ=255)
                                                            cTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGc                            >  1:2503532/1‑93 (MQ=255)
                                                            cTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGc                            >  2:3433409/1‑93 (MQ=255)
                                                              ttttGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGCCCg                          >  2:3413951/1‑93 (MQ=255)
                                                               tttGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGGAAAAATACCAGGTTCGGCATTCCAGGCCCCAGGCCGa                         >  1:2623244/1‑93 (MQ=255)
                                                               tttGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGa                         >  2:1667516/1‑93 (MQ=255)
                                                                 tGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGt                       <  2:1223249/93‑1 (MQ=255)
                                                                  gTTCGCGTCCGCGAAACCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTa                      <  2:1670389/93‑1 (MQ=255)
                                                                   ttCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTaa                     <  1:1276367/93‑1 (MQ=255)
                                                                     cgcgTCCGCTTATCCACCAGGTCAGCCCGAGCAATCCGGCAGGGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAAc                   <  1:711257/93‑1 (MQ=255)
                                                                      gcgTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAAcc                  >  1:1705104/1‑93 (MQ=255)
                                                                        gTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGa                <  2:1106978/93‑1 (MQ=255)
                                                                        gTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGa                <  2:1900954/93‑1 (MQ=255)
                                                                         tCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAg               <  1:3716652/93‑1 (MQ=255)
                                                                           cgcgTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCa             <  1:3962094/93‑1 (MQ=255)
                                                                            gcgTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAc            <  2:603367/93‑1 (MQ=255)
                                                                            gcgTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAc            <  2:4512116/93‑1 (MQ=255)
                                                                               tATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAcggc         >  2:692467/1‑93 (MQ=255)
                                                                               tATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAcggc         <  1:2948779/93‑1 (MQ=255)
                                                                                ttCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAcggcg        <  1:2643096/92‑1 (MQ=255)
                                                                                aTCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAcggcg        <  2:3872687/93‑1 (MQ=255)
                                                                                 tCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAcggcgg       <  1:487099/93‑1 (MQ=255)
                                                                                 tCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAcggcgg       <  2:1303504/93‑1 (MQ=255)
                                                                                 tCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAcggcgg       >  2:4607619/1‑93 (MQ=255)
                                                                                  ccaccaGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACggcggc      <  2:2001724/93‑1 (MQ=255)
                                                                                   caccaGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGgcggcg     <  2:2120381/93‑1 (MQ=255)
                                                                                    accaGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGgcgc    <  1:1756371/93‑1 (MQ=255)
                                                                                     ccaGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCt   >  1:738204/1‑93 (MQ=255)
                                                                                     ccaGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCt   <  2:2920260/93‑1 (MQ=255)
                                                                                     ccaGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCt   <  2:3069023/93‑1 (MQ=255)
                                                                                      caGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCtt  >  2:1212578/1‑93 (MQ=255)
                                                                                          |                                                                                        
ACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCTT  >  NC_000913/1962015‑1962193

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCT  >  NC_000913/1962012‑1962192
                                                                                             |                                                                                       
TCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGT                                                                                         >  SRR4302544.3042978/1‑94 (MQ=60)
  CACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCA                                                                                       >  SRR4302544.903446/1‑94 (MQ=60)
  CACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCA                                                                                       <  SRR4302544.1483488/94‑1 (MQ=60)
   ACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAG                                                                                      >  SRR4302544.452604/1‑94 (MQ=60)
    CGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGC                                                                                     >  SRR4302544.2521865/1‑94 (MQ=60)
     GTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCC                                                                                    >  SRR4302544.2720410/1‑94 (MQ=60)
       CGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCG                                                                                  >  SRR4302544.1653194/1‑94 (MQ=60)
       CGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCG                                                                                  >  SRR4302544.2079440/1‑94 (MQ=60)
        GCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGA                                                                                 <  SRR4302544.4521634/94‑1 (MQ=60)
         CTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAG                                                                                >  SRR4302544.444609/1‑94 (MQ=60)
             GACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAAT                                                                            >  SRR4302544.35782/1‑94 (MQ=60)
             GACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCATATCCACCAGGTCAGCCCGAGCAAC                                                                            >  SRR4302544.966898/1‑94 (MQ=60)
               CAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCCGGTCAGCCCGAGCAATCC                                                                          >  SRR4302544.4124614/1‑94 (MQ=60)
               CAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCC                                                                          >  SRR4302544.668438/1‑94 (MQ=60)
                  AGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGC                                                                       <  SRR4302544.4319944/94‑1 (MQ=60)
                   GGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCA                                                                      <  SRR4302544.1246573/94‑1 (MQ=60)
                   CGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCA                                                                      <  SRR4302544.3170485/94‑1 (MQ=60)
                     TATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGT                                                                    <  SRR4302544.4659536/94‑1 (MQ=60)
                     TATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGT                                                                    <  SRR4302544.4659537/94‑1 (MQ=60)
                     TATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGT                                                                    <  SRR4302544.755139/94‑1 (MQ=60)
                       TTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGGTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCACGCAGTGA                                                                  >  SRR4302544.4086854/1‑94 (MQ=60)
                       TTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGA                                                                  >  SRR4302544.4086855/1‑94 (MQ=60)
                       TTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGA                                                                  >  SRR4302544.4086856/1‑94 (MQ=60)
                         ATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAAC                                                                >  SRR4302544.1367933/1‑94 (MQ=60)
                                GCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAA                                                         >  SRR4302544.4439319/1‑94 (MQ=60)
                                GCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAA                                                         >  SRR4302544.4104968/1‑94 (MQ=60)
                                GCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAA                                                         >  SRR4302544.103741/1‑94 (MQ=60)
                                GCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAA                                                         >  SRR4302544.4082321/1‑94 (MQ=60)
                                 CCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAA                                                        >  SRR4302544.72532/1‑94 (MQ=60)
                                  CATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAAT                                                       <  SRR4302544.1875664/94‑1 (MQ=60)
                                  CATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAAT                                                       >  SRR4302544.3876436/1‑94 (MQ=60)
                                  CATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAAT                                                       >  SRR4302544.2807613/1‑94 (MQ=60)
                                    TTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATAC                                                     <  SRR4302544.4104752/94‑1 (MQ=60)
                                    TTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATAC                                                     <  SRR4302544.2986292/94‑1 (MQ=60)
                                     TTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCCGGTCAGCCCGAGCAATCCGGCAGTGAACCGCAAAAATACC                                                    >  SRR4302544.2115340/1‑94 (MQ=60)
                                       TTACCGGTTTGGGTTCGGGTGGCGCTTTTTGTTCGCGTCCGCGTATTCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATAACAG                                                  >  SRR4302544.2196534/1‑94 (MQ=60)
                                       TTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAG                                                  <  SRR4302544.454090/94‑1 (MQ=60)
                                         ACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGT                                                >  SRR4302544.2285550/1‑94 (MQ=60)
                                         ACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGT                                                <  SRR4302544.879102/94‑1 (MQ=60)
                                            GGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCG                                             <  SRR4302544.3613959/94‑1 (MQ=60)
                                                 GGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATT                                        <  SRR4302544.3972069/94‑1 (MQ=60)
                                                 GGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATT                                        <  SRR4302544.1124635/94‑1 (MQ=60)
                                                 GGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATT                                        >  SRR4302544.1984519/1‑94 (MQ=60)
                                                  GGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTC                                       >  SRR4302544.1886634/1‑94 (MQ=60)
                                                   GTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCC                                      <  SRR4302544.949214/94‑1 (MQ=60)
                                                      CGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGG                                   <  SRR4302544.1661002/94‑1 (MQ=60)
                                                         CTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCAC                                <  SRR4302544.4222375/94‑1 (MQ=60)
                                                         CTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCAC                                <  SRR4302544.1241211/94‑1 (MQ=60)
                                                           GGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCA                              >  SRR4302544.3465556/1‑94 (MQ=60)
                                                             CGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGG                            <  SRR4302544.1550076/94‑1 (MQ=60)
                                                              GCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGC                           >  SRR4302544.2527533/1‑94 (MQ=60)
                                                                 TTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGGAAAAATACCAGGTTCGGCATTCCAGGCCCCAGGCCGA                        >  SRR4302544.2648398/1‑94 (MQ=60)
                                                                   TTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGT                      <  SRR4302544.1472232/94‑1 (MQ=60)
                                                                      TTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAA                   <  SRR4302544.1288935/94‑1 (MQ=60)
                                                                        CGCGTCCGCTTATCCACCAGGTCAGCCCGAGCAATCCGGCAGGGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACC                 <  SRR4302544.718309/94‑1 (MQ=60)
                                                                        CGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACC                 >  SRR4302544.1721919/1‑94 (MQ=60)
                                                                            TCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGC             <  SRR4302544.3753625/94‑1 (MQ=60)
                                                                              CGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCAC           <  SRR4302544.4001496/94‑1 (MQ=60)
                                                                               GCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACG          <  SRR4302544.3872504/94‑1 (MQ=60)
                                                                                  TATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCG       <  SRR4302544.2977103/94‑1 (MQ=60)
                                                                                   TTCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGG      <  SRR4302544.2668438/94‑1 (MQ=60)
                                                                                    TCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGC     <  SRR4302544.491872/94‑1 (MQ=60)
                                                                                       ACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCT  >  SRR4302544.745428/1‑94 (MQ=60)
                                                                                       ACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCT  <  SRR4302544.1773561/94‑1 (MQ=60)
                                                                                             |                                                                                       
TCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACCAGGCCGAGTAAACCGAGCACGGCGGCGCT  >  NC_000913/1962012‑1962192

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑