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
A3 F53 I1 R1 62 81.2 3465250 98.6% 3416736 145.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 2,958,523 C→T A428V (GCA→GTA)  PP_2589 → aldehyde dehydrogenase family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC2,958,5230CT100.0% 249.8 / NA 72A428V (GCA→GTA) PP_2589aldehyde dehydrogenase family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (36/36);  total (36/36)

TACATCGAGCCGACCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGCAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGCCGCG  >  NC_002947_CJ‑RC/2958378‑2958666
                                                                                                                                                 |                                                                                                                                               
tACATCGAGCCGACCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAg                                                                                                                                               >  2:240431/1‑148 (MQ=255)
  cATCGAGCCGACCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAg                                                                                                                                               <  4:338213/146‑1 (MQ=255)
      gAGCCGACCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCgg                                                                                                                                         >  8:426150/1‑148 (MQ=255)
               aTTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGc                                                                                                                                 >  1:239600/1‑147 (MQ=255)
                tttttGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGcga                                                                                                                               >  3:80715/1‑148 (MQ=255)
                tttttGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGcga                                                                                                                               <  3:346383/148‑1 (MQ=255)
                     gCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCgacgac                                                                                                                           <  8:356646/147‑1 (MQ=255)
                        ggTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTc                                                                                                                        >  4:243649/1‑147 (MQ=255)
                         gtgtCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCaa                                                                                                                      <  4:370058/148‑1 (MQ=255)
                         gtgtCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCaa                                                                                                                      <  4:309771/148‑1 (MQ=255)
                          tgtCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAAc                                                                                                                     >  4:377672/1‑148 (MQ=255)
                            tCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCa                                                                                                                   <  5:363306/148‑1 (MQ=255)
                            tCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCa                                                                                                                   <  1:241712/148‑1 (MQ=255)
                            tCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCa                                                                                                                   <  8:127056/148‑1 (MQ=255)
                               aGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGt                                                                                                                >  4:49999/1‑148 (MQ=255)
                               aGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAAAGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGt                                                                                                                >  6:42646/1‑148 (MQ=255)
                                      cATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCgg                                                                                                         <  1:186524/148‑1 (MQ=255)
                                       aTGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCggg                                                                                                        >  7:172645/1‑148 (MQ=255)
                                        tGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGt                                                                                                       <  1:300683/148‑1 (MQ=255)
                                              tGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGcgcg                                                                                                 >  2:76959/1‑148 (MQ=255)
                                                gcgcgcGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGcgcg                                                                                                 <  6:276508/146‑1 (MQ=255)
                                                gcgcgcGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCggg                                                                                               <  7:426150/148‑1 (MQ=255)
                                                   ggcgAGGAGGTGTTGGGCCCGGTTCGGGCGGTCAGCGCCTTCGACACGGAAGACGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTTGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGt                                                                                            <  2:416577/147‑1 (MQ=255)
                                                   cgcgAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGt                                                                                            <  3:377672/148‑1 (MQ=255)
                                                      gaggagGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGa                                                                                         <  2:239802/148‑1 (MQ=255)
                                                          aggTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGc                                                                                     >  4:402077/1‑148 (MQ=255)
                                                            gtgtTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCg                                                                                   >  3:200028/1‑148 (MQ=255)
                                                             tgtTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCgg                                                                                  >  4:404689/1‑148 (MQ=255)
                                                               ttCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTa                                                                                >  1:400491/1‑148 (MQ=255)
                                                                tCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTAc                                                                               >  4:105757/1‑148 (MQ=255)
                                                                     ccGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTAt                                                                          >  3:85596/1‑148 (MQ=255)
                                                                           cTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGATGa                                                                    <  3:116468/148‑1 (MQ=255)
                                                                             ggCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGaa                                                                   >  4:253004/1‑147 (MQ=255)
                                                                               cGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAaca                                                                 >  8:209043/1‑147 (MQ=255)
                                                                               cGGTCAGCGCCTTCGACACGGAAGAAGAAGCAGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGCTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTACCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAaca                                                                 >  8:322646/1‑147 (MQ=255)
                                                                                 gTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAg                                                              <  1:240431/148‑1 (MQ=255)
                                                                                  tCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGt                                                             >  4:357839/1‑148 (MQ=255)
                                                                                  tCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGt                                                             <  7:209043/148‑1 (MQ=255)
                                                                                   cAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTc                                                            >  3:166596/1‑148 (MQ=255)
                                                                                     gcgcCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGa                                                          <  3:243649/148‑1 (MQ=255)
                                                                                     gcgcCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGa                                                          <  1:193965/148‑1 (MQ=255)
                                                                                     gcgcCGTCGAGACGGAAGAAGAAGCCGTGCGCCTGGCCGGCGACTGCATCGAGGGCCTGGTAGCGTCGGGGTGGAGCGACGACTTCAACCAGGGGCACCGGGGAGCGCGGGGGTTGTAAGGGGGTACCGTAGCGGTGATCACAggc                                                            >  4:10860/1‑144 (MQ=255)
                                                                                        ccTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATgc                                                       >  6:198074/1‑148 (MQ=255)
                                                                                             gACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTg                                                   >  7:109776/1‑147 (MQ=255)
                                                                                              acacGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGa                                                 <  2:416753/148‑1 (MQ=255)
                                                                                                acGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGAtg                                               <  2:400491/148‑1 (MQ=255)
                                                                                                 cGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGgt                                                                                                                                        >  8:141971/1‑58 (MQ=255)
                                                                                                 cGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGgt                                                                                                                                        <  7:141971/58‑1 (MQ=255)
                                                                                                 cGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGt                                                             <  1:237619/133‑1 (MQ=255)
                                                                                                 cGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGt                                                             >  2:237619/1‑133 (MQ=255)
                                                                                                 cGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGAtgt                                              >  5:5420/1‑148 (MQ=255)
                                                                                                 cGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGAtgt                                              <  3:404689/148‑1 (MQ=255)
                                                                                                  ggAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGAtgtg                                             <  3:253004/148‑1 (MQ=255)
                                                                                                      gaagaagCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCt                                                    <  5:140739/137‑1 (MQ=255)
                                                                                                      gaagaagCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCt                                                    >  6:140739/1‑137 (MQ=255)
                                                                                                          aagCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATCTGACGGTGcc                                     >  5:24793/1‑148 (MQ=255)
                                                                                                           agCCGTGCACCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCg                                    >  8:268145/1‑148 (MQ=255)
                                                                                                               gTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCg                                <  5:42646/148‑1 (MQ=255)
                                                                                                                tGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCgg                               <  5:91483/148‑1 (MQ=255)
                                                                                                                  cgcCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTg                             <  6:5420/148‑1 (MQ=255)
                                                                                                                  cgcCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTg                             <  6:39625/148‑1 (MQ=255)
                                                                                                                    ccTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTggg                           <  8:307348/148‑1 (MQ=255)
                                                                                                                    ccTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTggg                           <  8:172645/148‑1 (MQ=255)
                                                                                                                       ggCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTggggg                         >  7:249145/1‑147 (MQ=255)
                                                                                                                       ggCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTggggg                         >  4:119401/1‑147 (MQ=255)
                                                                                                                            aCGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAg                     >  3:66692/1‑146 (MQ=255)
                                                                                                                            aCGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCa                   <  3:260796/148‑1 (MQ=255)
                                                                                                                                    aTCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGt           >  6:290776/1‑148 (MQ=255)
                                                                                                                                    aTCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGATGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGAGGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGt           >  2:423755/1‑148 (MQ=255)
                                                                                                                                         tGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGc      >  6:18552/1‑148 (MQ=255)
                                                                                                                                           gCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGcc     <  7:268145/147‑1 (MQ=255)
                                                                                                                                             cTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGCcgcg  <  8:246430/148‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                               
TACATCGAGCCGACCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGCAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGCCGCG  >  NC_002947_CJ‑RC/2958378‑2958666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AACTACATCGAGCCGACCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGCAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGCCGCGATCT  >  NC_002947_CJ‑RC/2958375‑2958670
                                                                                                                                                    |                                                                                                                                                   
AACTACATCGAGCCGACCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAG                                                                                                                                                   <  NB501016:282:H2V7GAFX2:1:21104:20911:13251/151‑1 (MQ=60)
                CCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCG                                                                                                                                    >  NB501016:282:H2V7GAFX2:1:21103:14437:8749/1‑150 (MQ=60)
                 CATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGAC                                                                                                                                  >  NB501016:282:H2V7GAFX2:2:11202:18924:13548/1‑151 (MQ=60)
                  ATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACG                                                                                                                                 <  NB501016:282:H2V7GAFX2:2:21301:12998:2290/151‑1 (MQ=60)
                              GTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGG                                                                                                                     <  NB501016:282:H2V7GAFX2:3:21601:23345:7969/151‑1 (MQ=60)
                              GTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGG                                                                                                                     <  NB501016:282:H2V7GAFX2:1:21103:24446:14956/151‑1 (MQ=60)
                                        GCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGT                                                                                                           <  NB501016:282:H2V7GAFX2:1:11306:9519:10462/151‑1 (MQ=60)
                                        GCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGT                                                                                                           >  NB501016:282:H2V7GAFX2:4:11604:22678:11027/1‑151 (MQ=60)
                                          ATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAG                                                                                                         <  NB501016:282:H2V7GAFX2:1:21201:12824:12001/151‑1 (MQ=60)
                                                  GGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCG                                                                                                 <  NB501016:282:H2V7GAFX2:4:21609:8318:19369/151‑1 (MQ=60)
                                                     GCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTG                                                                                              <  NB501016:282:H2V7GAFX2:2:21306:4937:12165/151‑1 (MQ=60)
                                                             AGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGG                                                                                      >  NB501016:282:H2V7GAFX2:2:11309:23090:18228/1‑151 (MQ=60)
                                                                TGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTAC                                                                                   >  NB501016:282:H2V7GAFX2:1:21307:7098:4074/1‑151 (MQ=60)
                                                                      GCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATC                                                                             >  NB501016:282:H2V7GAFX2:2:11203:14476:10090/1‑151 (MQ=60)
                                                                             ACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGATGAAC                                                                      <  NB501016:282:H2V7GAFX2:2:11208:19606:11491/151‑1 (MQ=60)
                                                                                   GGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTC                                                                <  NB501016:282:H2V7GAFX2:1:21103:7516:11150/151‑1 (MQ=60)
                                                                                    GTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCG                                                               <  NB501016:282:H2V7GAFX2:4:11610:16880:12931/151‑1 (MQ=60)
                                                                                    GTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCG                                                               >  NB501016:282:H2V7GAFX2:2:11304:3252:14140/1‑151 (MQ=60)
                                                                                       AGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATG                                                            <  NB501016:282:H2V7GAFX2:1:11307:21676:16461/151‑1 (MQ=60)
                                                                                       AGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATG                                                            <  NB501016:282:H2V7GAFX2:2:21105:15718:6551/151‑1 (MQ=60)
                                                                                              TCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGG                                                      >  NB501016:282:H2V7GAFX2:4:11506:17095:7448/1‑150 (MQ=60)
                                                                                                  CACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTG                                                 >  NB501016:282:H2V7GAFX2:3:11401:18888:18622/1‑151 (MQ=60)
                                                                                                  CACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCG                                                               <  NB501016:282:H2V7GAFX2:1:21103:16072:2729/137‑1 (MQ=60)
                                                                                                  CACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGT                                                                                                                                          <  NB501016:282:H2V7GAFX2:4:11511:12822:9700/62‑1 (MQ=60)
                                                                                                   ACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGA                                                <  NB501016:282:H2V7GAFX2:2:21310:21804:16541/151‑1 (MQ=60)
                                                                                                    CGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGAC                                               <  NB501016:282:H2V7GAFX2:2:21106:14217:18613/151‑1 (MQ=60)
                                                                                                       AAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGG                                                      <  NB501016:282:H2V7GAFX2:3:11512:26708:5871/141‑1 (MQ=60)
                                                                                                           AGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATCTGACGGTGCCG                                        >  NB501016:282:H2V7GAFX2:3:11405:20373:4730/1‑151 (MQ=60)
                                                                                                                 CGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGT                                  <  NB501016:282:H2V7GAFX2:3:11408:15414:5911/151‑1 (MQ=60)
                                                                                                                  GTGCGCCTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTG                                 <  NB501016:282:H2V7GAFX2:3:11504:14501:8318/151‑1 (MQ=60)
                                                                                                                        CTGGCCAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGC                            >  NB501016:282:H2V7GAFX2:4:21405:15697:4018/1‑150 (MQ=60)
                                                                                                                             CAACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGC                        >  NB501016:282:H2V7GAFX2:2:11112:16752:6998/1‑149 (MQ=60)
                                                                                                                              AACGACAGCATCTATGGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGT                     <  NB501016:282:H2V7GAFX2:2:21108:4084:6512/151‑1 (MQ=60)
                                                                                                                                             GGCCTGGTAGCCTCGGTGTGGAGCGACGACTTCAACCTGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGCCGC       <  NB501016:282:H2V7GAFX2:4:21408:5282:4787/150‑1 (MQ=60)
                                                                                                                                                  GGTAGCCTCGGTGGGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGCCGCGATCT  <  NB501016:282:H2V7GAFX2:2:11206:24924:15491/150‑1 (MQ=60)
                                                                                                                                                    |                                                                                                                                                   
AACTACATCGAGCCGACCATTTTTGCCGGTGTCGAGGGCCGCATGAGCCTGGCGCGCGAGGAGGTGTTCGGCCCGGTACTGGCGGTCAGCGCCTTCGACACGGAAGAAGAAGCCGTGCGCCTGGCCAACGACAGCATCTATGGCCTGGCAGCCTCGGTGTGGAGCGACGACTTCAACCAGGTGCACCGGGTAGCGCGGGCGTTGAAAGCCGGTACCGTATCGGTGAACACAGTCGATGCGCTGGATGTGACGGTGCCGTTCGGTGGGGGCAAGCAGTCGGGGTTTGGCCGCGATCT  >  NC_002947_CJ‑RC/2958375‑2958670

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑