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 3,494,690 A→G A17A (GCA→GCG)  nirC → Nitrite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,494,6900AG99.1% 337.1 / ‑4.5 107A17A (GCA→GCG) nirCNitrite transporter
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (82/24);  total (82/25)
Fisher's exact test for biased strand distribution p-value = 2.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

Only 100 of 108 total aligned reads displayed.

GTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCACGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCAC  >  NC_000913/3494602‑3494779
                                                                                        |                                                                                         
gTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGcc                                                                                       <  1:594709/93‑1 (MQ=255)
    tATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTc                                                                                   >  1:2864204/1‑93 (MQ=255)
     aTTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCg                                                                                  >  1:4527485/1‑93 (MQ=255)
       tttttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGc                                                                                >  2:960734/1‑93 (MQ=255)
       tttttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGc                                                                                <  2:4141762/93‑1 (MQ=255)
       tttttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGc                                                                                >  1:3352602/1‑93 (MQ=255)
       tttttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGc                                                                                >  2:1624462/1‑93 (MQ=255)
       tttttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGc                                                                                >  1:4727395/1‑93 (MQ=255)
        ttttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCa                                                                               >  1:4272439/1‑93 (MQ=255)
         tttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCaa                                                                              >  1:2833246/1‑93 (MQ=255)
         tttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCaa                                                                              >  1:683448/1‑93 (MQ=255)
          ttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCaaa                                                                             >  1:340895/1‑93 (MQ=255)
          ttGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCaaa                                                                             >  2:4006651/1‑93 (MQ=255)
           tGTTTTTATTTTTTAAAGGTTAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAAt                                                                            >  1:2849130/1‑93 (MQ=255)
            gTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATa                                                                           <  1:4412419/93‑1 (MQ=255)
            gTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATa                                                                           <  1:4412418/93‑1 (MQ=255)
             tttttATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATaa                                                                          <  1:4644621/93‑1 (MQ=255)
             tttttATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATaa                                                                          >  2:3157794/1‑93 (MQ=255)
             tttttATTTTTTAAAGGATAATCAAATGTTTACAGACACTAATAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATaa                                                                          >  2:1228375/1‑93 (MQ=255)
               tttATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAAcc                                                                        >  1:3548294/1‑93 (MQ=255)
               tttATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAAcc                                                                        <  1:1215729/93‑1 (MQ=255)
                 tATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAAcccc                                                                      >  1:1510510/1‑92 (MQ=255)
                        tAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCt                                                               >  1:2721209/1‑93 (MQ=255)
                        tAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCt                                                               >  1:2639901/1‑93 (MQ=255)
                         aaaGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCtt                                                              >  1:2897660/1‑93 (MQ=255)
                         aaaGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCtt                                                              >  2:599710/1‑93 (MQ=255)
                          aaGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCttt                                                             >  2:3364275/1‑93 (MQ=255)
                            ggATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTg                                                           <  1:4099093/93‑1 (MQ=255)
                            ggATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTg                                                           <  2:3835642/93‑1 (MQ=255)
                            ggATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTg                                                           >  2:2675026/1‑93 (MQ=255)
                            ggATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTg                                                           <  2:3558245/93‑1 (MQ=255)
                            ggATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCACATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTg                                                           >  2:3919617/1‑93 (MQ=255)
                             gATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTgg                                                          >  2:240329/1‑93 (MQ=255)
                             gATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTgg                                                          >  2:2962401/1‑93 (MQ=255)
                             gATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTgg                                                          >  2:3706241/1‑93 (MQ=255)
                             gATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCCCTCGGCTTTTgg                                                          >  1:2932472/1‑93 (MQ=255)
                               tAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGt                                                        >  1:2503366/1‑93 (MQ=255)
                               tAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGt                                                        >  2:678220/1‑93 (MQ=255)
                                aaTCAAATGTTTAGAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTc                                                       >  1:3137873/1‑93 (MQ=255)
                                aaTCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTc                                                       >  1:4671273/1‑93 (MQ=255)
                                aaTCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTc                                                       >  2:1651133/1‑93 (MQ=255)
                                aaTCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTc                                                       <  1:3983305/93‑1 (MQ=255)
                                 aTCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCa                                                      >  2:2907303/1‑93 (MQ=255)
                                  tCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTccg                                                     >  2:1320329/1‑91 (MQ=255)
                                  tCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAg                                                     >  1:2246822/1‑93 (MQ=255)
                                   cAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAgt                                                    >  1:2598300/1‑92 (MQ=255)
                                   cAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGc                                                    >  1:2598301/1‑93 (MQ=255)
                                    aaaTGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCaccc                                                   >  1:1432853/1‑90 (MQ=255)
                                    aaaTGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCt                                                   >  2:3671484/1‑93 (MQ=255)
                                    aaaTGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCt                                                   >  2:523154/1‑93 (MQ=255)
                                    aaaTGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCt                                                   >  2:3671485/1‑93 (MQ=255)
                                    aaaTGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTAGGCAAATAACCCGCTCGGCTTTTGGGTCAGCt                                                   >  2:4038669/1‑93 (MQ=255)
                                     aaTGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTc                                                  >  1:900322/1‑93 (MQ=255)
                                     aaTGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTc                                                  >  2:1688850/1‑93 (MQ=255)
                                      aTGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTcc                                                 >  1:2455539/1‑93 (MQ=255)
                                       tGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCg                                                >  2:2304177/1‑93 (MQ=255)
                                       tGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCg                                                >  1:1612053/1‑93 (MQ=255)
                                        gTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGc                                               >  1:1101499/1‑93 (MQ=255)
                                            aCAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATg                                           <  1:2070008/93‑1 (MQ=255)
                                            aCAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATg                                           <  1:4263082/93‑1 (MQ=255)
                                              aGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggc                                         >  2:4054399/1‑93 (MQ=255)
                                              aGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggc                                         >  2:2900526/1‑93 (MQ=255)
                                               gACACTATTAATAAGTGTGCGGCTAACGCTGTGCGCATTGTTCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggcg                                        >  2:3844369/1‑93 (MQ=255)
                                               gACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggcg                                        <  2:1910956/93‑1 (MQ=255)
                                               gACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggcg                                        >  1:3794673/1‑93 (MQ=255)
                                               gACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggcg                                        >  1:4344532/1‑93 (MQ=255)
                                               gACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggcg                                        >  2:1321545/1‑93 (MQ=255)
                                                acacTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggcgg                                       <  2:2374793/93‑1 (MQ=255)
                                                acacTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATggcgg                                       >  2:250348/1‑93 (MQ=255)
                                                    tATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGgcgc                                   >  1:162971/1‑93 (MQ=255)
                                                    tATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGgcgc                                   >  2:902302/1‑93 (MQ=255)
                                                     aTTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGcgcg                                  >  2:2966164/1‑93 (MQ=255)
                                                       taataaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTa                                >  1:37497/1‑93 (MQ=255)
                                                       taataaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTa                                <  1:1854961/93‑1 (MQ=255)
                                                        aataaGTGTGCGGCTAACGCTGTGCGCATTGCGCGCCTGTTGTTAAATAACCTGCTCGGCGTTTGTGTCAGCTCCGCCATGGCGGTcgcggtg                               >  2:4199134/1‑90 (MQ=255)
                                                        aataaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAt                               >  1:1816348/1‑93 (MQ=255)
                                                         ataaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGCGTCAGCTCCGCCATGGCGGGCGCGTAtg                              >  2:117264/1‑93 (MQ=255)
                                                          taaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAtgt                             >  2:3123121/1‑93 (MQ=255)
                                                          taaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAtgt                             <  2:3205388/93‑1 (MQ=255)
                                                          taaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAtgg                             >  1:3453775/1‑92 (MQ=255)
                                                          aaaGTTTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTGTGGGTCAGCTCCGCCATGGCGGGCGCGTAtgt                             <  1:3464245/92‑1 (MQ=255)
                                                          aaaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAtgt                             <  1:3464246/92‑1 (MQ=255)
                                                           aaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAtgtg                            <  1:3233892/93‑1 (MQ=255)
                                                           aaGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAtgtg                            >  2:223584/1‑93 (MQ=255)
                                                             gtgtGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTggg                          >  2:2927255/1‑93 (MQ=255)
                                                             gtgtGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTggg                          <  2:1546108/93‑1 (MQ=255)
                                                               gtgCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTc                        >  1:2805253/1‑93 (MQ=255)
                                                                tgCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCt                       >  1:3600861/1‑93 (MQ=255)
                                                                tgCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCt                       <  1:3706789/93‑1 (MQ=255)
                                                                   ggCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGGCTTgg                    >  2:399149/1‑93 (MQ=255)
                                                                     cTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGa                  >  1:1477504/1‑93 (MQ=255)
                                                                        aCGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGatca               >  2:4121187/1‑93 (MQ=255)
                                                                         cGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGatcat              <  2:3880604/93‑1 (MQ=255)
                                                                           cTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATcc            >  1:2803227/1‑93 (MQ=255)
                                                                              cgcgcATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGTCGCGTATGTGGGTCTTGGGATCATCCTgt         >  1:3893571/1‑92 (MQ=255)
                                                                               gcgcATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGAt        >  2:2675260/1‑93 (MQ=255)
                                                                               gcgcATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGAt        <  1:574465/93‑1 (MQ=255)
                                                                                    ttGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCa   >  2:331458/1‑93 (MQ=255)
                                                                                    ttGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCa   >  1:1640554/1‑93 (MQ=255)
                                                                                     tGCACGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCAc  <  1:1554081/93‑1 (MQ=255)
                                                                                        |                                                                                         
GTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCACGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCAC  >  NC_000913/3494602‑3494779

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TTTTTGTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCACGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCACGCTC  >  NC_000913/3494597‑3494783
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TTTTTGTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCG                                                                                               <  SRR4302544.1010013/94‑1 (MQ=60)
     GTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCT                                                                                          <  SRR4302544.600544/94‑1 (MQ=60)
        TTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTC                                                                                       >  SRR4302544.2891854/1‑94 (MQ=60)
         TATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCG                                                                                      >  SRR4302544.4572789/1‑94 (MQ=60)
           TTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGC                                                                                    >  SRR4302544.4774050/1‑94 (MQ=60)
           TTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGC                                                                                    >  SRR4302544.3384597/1‑94 (MQ=60)
            TTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCA                                                                                   >  SRR4302544.4316055/1‑94 (MQ=60)
             TTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAA                                                                                  >  SRR4302544.690243/1‑94 (MQ=60)
             TTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAA                                                                                  >  SRR4302544.2860618/1‑94 (MQ=60)
              TTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAA                                                                                 >  SRR4302544.344423/1‑94 (MQ=60)
               TTGTTTTTATTTTTTAAAGGTTAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAAT                                                                                >  SRR4302544.2876652/1‑94 (MQ=60)
                 GTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAA                                                                              <  SRR4302544.4456967/94‑1 (MQ=60)
                 GTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAA                                                                              <  SRR4302544.4456966/94‑1 (MQ=60)
                  TTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAAC                                                                             <  SRR4302544.4690612/94‑1 (MQ=60)
                   TTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACC                                                                            >  SRR4302544.3582275/1‑94 (MQ=60)
                    TTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCC                                                                           <  SRR4302544.1227762/94‑1 (MQ=60)
                     TTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCC                                                                          >  SRR4302544.1525483/1‑94 (MQ=60)
                            TTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCT                                                                   >  SRR4302544.2747410/1‑94 (MQ=60)
                            TTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCT                                                                   >  SRR4302544.2665207/1‑94 (MQ=60)
                             TAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTT                                                                  >  SRR4302544.2925567/1‑94 (MQ=60)
                                 GGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGG                                                              <  SRR4302544.4139886/94‑1 (MQ=60)
                                 GGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCCCTCGGCTTTTGG                                                              >  SRR4302544.2960651/1‑94 (MQ=60)
                                   ATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGT                                                            >  SRR4302544.2527366/1‑94 (MQ=60)
                                    TAATCAAATGTTTAGAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTC                                                           >  SRR4302544.3167687/1‑94 (MQ=60)
                                    TAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTC                                                           >  SRR4302544.4717443/1‑94 (MQ=60)
                                     AATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCA                                                          <  SRR4302544.4022951/94‑1 (MQ=60)
                                      ATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAG                                                         >  SRR4302544.2267948/1‑94 (MQ=60)
                                       TCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGT                                                        >  SRR4302544.2623277/1‑94 (MQ=60)
                                       TCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGC                                                        >  SRR4302544.2623278/1‑94 (MQ=60)
                                        CAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAccc                                                       >  SRR4302544.1447111/1‑91 (MQ=60)
                                         AAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTC                                                      >  SRR4302544.909229/1‑94 (MQ=60)
                                          AATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCC                                                     >  SRR4302544.2478965/1‑94 (MQ=60)
                                           ATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCG                                                    >  SRR4302544.1627947/1‑94 (MQ=60)
                                            TGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGC                                                   >  SRR4302544.2959508/1‑94 (MQ=60)
                                            TGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGC                                                   >  SRR4302544.1112470/1‑94 (MQ=60)
                                                 ACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGG                                              <  SRR4302544.4306566/94‑1 (MQ=60)
                                                 ACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGG                                              <  SRR4302544.2089890/94‑1 (MQ=60)
                                                   AGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCG                                            >  SRR4302544.4388707/1‑94 (MQ=60)
                                                   AGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCG                                            >  SRR4302544.3832242/1‑94 (MQ=60)
                                                        CTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGC                                       >  SRR4302544.164562/1‑94 (MQ=60)
                                                           TTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTA                                    >  SRR4302544.37866/1‑94 (MQ=60)
                                                            TAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAT                                   >  SRR4302544.1834074/1‑94 (MQ=60)
                                                            TAATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTAT                                   <  SRR4302544.1872901/94‑1 (MQ=60)
                                                              ATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGG                                 >  SRR4302544.3486748/1‑94 (MQ=60)
                                                              ATAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGGATGT                                 >  SRR4302544.2385653/1‑94 (MQ=60)
                                                               AAAGTTTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTGTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTG                                <  SRR4302544.3497292/94‑1 (MQ=60)
                                                               AAAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTG                                <  SRR4302544.3497293/94‑1 (MQ=60)
                                                                AAGTGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGG                               <  SRR4302544.3264847/94‑1 (MQ=60)
                                                                   TGTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTC                            >  SRR4302544.2832299/1‑94 (MQ=60)
                                                                    GTGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCT                           >  SRR4302544.3635654/1‑94 (MQ=60)
                                                                     TGCGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTT                          <  SRR4302544.3743674/94‑1 (MQ=60)
                                                                       CGGCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGCGGGTCTTGG                        >  SRR4302544.2459300/1‑94 (MQ=60)
                                                                         GCTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGA                      >  SRR4302544.1492114/1‑94 (MQ=60)
                                                                          CTAACGCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGAT                     >  SRR4302544.53523/1‑94 (MQ=60)
                                                                               GCTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCC                >  SRR4302544.2830249/1‑94 (MQ=60)
                                                                                CTGCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGGCTTGGGATCATCCT               >  SRR4302544.3900146/1‑94 (MQ=60)
                                                                                  GCGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGTCGCGTATGTGGGTCTTGGGATCATCCTGT             >  SRR4302544.3932247/1‑94 (MQ=60)
                                                                                   CGCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGcatgcgggacgtgggattaatcttgt            >  SRR4302544.1745902/1‑68 (MQ=60)
                                                                                    GCGCATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATT           <  SRR4302544.580081/94‑1 (MQ=60)
                                                                                        ATTGCGCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCA       >  SRR4302544.1656720/1‑94 (MQ=60)
                                                                                          TGCACGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCACG     <  SRR4302544.1569546/94‑1 (MQ=60)
                                                                                             GCGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCACGCTC  >  SRR4302544.4102357/1‑94 (MQ=60)
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TTTTTGTTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTTTACAGACACTATTAATAAGTGTGCGGCTAACGCTGCGCGCATTGCACGCCTGTCGGCAAATAACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGGATCATCCTGATTTTCACGCTC  >  NC_000913/3494597‑3494783

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑