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 F104 I0 R1 106 58.2 1336546 90.2% 1205564 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,929,918 A→G 68.1% intergenic (‑1001/‑167) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,929,9180AG68.1% 153.8 / 95.3 129intergenic (‑1001/‑167)USA300HOU_1794/USA300HOU_1796hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (19/22);  new base G (49/38);  total (69/60)
Fisher's exact test for biased strand distribution p-value = 3.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.39e-01

Only 100 of 130 total aligned reads displayed.

GACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTAT  >  CP000730/1929779‑1930058
                                                                                                                                                 |                                                                                                                                            
gACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑GTTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAt                                                                                                                                             >  1:553498/1‑141 (MQ=255)
  cTGTGCTTGTATTTTTGCCGATGAAATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTg                                                                                                                                           <  1:626350/141‑1 (MQ=255)
    atgCTTGTATATTCACAGATGGCATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt                                                                                                                                        <  2:653165/140‑1 (MQ=255)
     tgCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACACCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGt                                                                                                                                        <  1:421486/141‑1 (MQ=255)
       cTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt                                                                                                                                     >  2:463506/1‑141 (MQ=255)
        ttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatta                                                                                                                                    <  2:356769/141‑5 (MQ=255)
        ttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatta                                                                                                                                    <  1:538881/141‑5 (MQ=255)
        ttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑CCTAATC‑ATTTTGGTTCACATCATAGCACCAGTCTTCAGTGGCTGTGCTGTTGCGtatta                                                                                                                                    >  2:282518/1‑140 (MQ=255)
        ttGTATATTCACAGATGGTATAACAATAGAGTCTCCTATCTCTCAGGCGTCAA‑‑TCGACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatta                                                                                                                                    <  1:102810/141‑5 (MQ=255)
         tGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGTCGCAGAGAGGAGGTGTA‑TAT‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGttttt                                                                                                                                    <  1:424911/141‑1 (MQ=255)
         tGTATATTCACAGCTGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattat                                                                                                                                   <  1:278405/141‑6 (MQ=255)
          gtatattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattata                                                                                                                                  >  1:242208/12‑138 (MQ=255)
            atattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTT‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatact                                                                                                                                >  1:572382/10‑136 (MQ=255)
             tattatcagatggtATAATAATAGTGTTTGCTATCTCTCGGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatactt                                                                                                                               <  1:120571/133‑7 (MQ=255)
             aatgcacagatggtAGAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑T‑TGGCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatactt                                                                                                                               <  1:594747/133‑7 (MQ=255)
               ttcacagatggtATAATGATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGCGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTGCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTAt                                                                                                                             >  1:469921/7‑141 (MQ=255)
               ttcacagatggtATAATAATAGAGTCGCGTATCTCTCAGGCGTCAATT‑‑GACGAAAAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAAGC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTAt                                                                                                                             >  1:429667/7‑141 (MQ=255)
                tcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTAtt                                                                                                                            >  2:91718/6‑141 (MQ=255)
                 cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg                                                                                                                           >  2:609170/5‑141 (MQ=255)
                 cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTACACTTATTg                                                                                                                           >  2:534203/5‑141 (MQ=255)
                   ccGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTgg                                                                                                                          <  1:448480/141‑1 (MQ=255)
                   ccGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTgg                                                                                                                          <  2:161790/141‑1 (MQ=255)
                   caggtggtataATAATAGAGTCGCCTATCTCTCATGCGTCAATT‑‑GACGGCGAGAGGGGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTCCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTTCGTATTATACTTATTGGc                                                                                                                         <  2:285528/134‑1 (MQ=255)
                    agatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt                                                                                                                        <  1:437605/140‑1 (MQ=255)
                     gatggtATAATAATAGAGTCGCCTATCTCTCAGGCTTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt                                                                                                                       <  2:536543/141‑2 (MQ=255)
                     gatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt                                                                                                                       >  2:272694/1‑140 (MQ=255)
                     gatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt                                                                                                                       >  2:508681/1‑140 (MQ=255)
                       tgttataATAATAGAGTCGTCTATCTCTCAGGCGTCAA‑‑TGGACGAATAGAGGAGGTCCATTAC‑T‑T‑T‑GCTAATC‑CTTTTCGTTCGCATCATAGCACCAGTCAGCAGTGGCTGTGCTGTGGCGTATTATACTTATTGGCTTAg                                                                                                                     <  2:270883/138‑1 (MQ=255)
                       tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                     <  1:612933/138‑4 (MQ=255)
                       tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                     <  2:415240/138‑4 (MQ=255)
                       tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                     <  2:197083/138‑4 (MQ=255)
                       tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTCCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAg                                                                                                                     >  1:649279/4‑141 (MQ=255)
                       tggtataATAATAGAGTCGCCTATCTCTCAGGAGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATTATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                     <  1:446155/138‑4 (MQ=255)
                       gagtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TTT‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                     <  1:638521/138‑4 (MQ=255)
                        ggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTGTACTTATTGGCttggt                                                                                                                    >  1:573848/3‑137 (MQ=255)
                        gatATAATAGTAGAGCCGCCTATCTCTCAGGCGACAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTAGTTCACACCATAGAACCAGGCAACAGTGGCTGTGGCATTGCGTGTTTTTcatcttcactaat                                                                                                                     >  2:625437/1‑129 (MQ=255)
                         gtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGCCATCAGTGGCTGTGCTGTTGCGTATTATACTGATTGGCTTAGTa                                                                                                                   >  1:74474/2‑141 (MQ=255)
                         atatAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGt                                                                                                                    >  1:652215/1‑141 (MQ=255)
                         atatAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGt                                                                                                                    >  1:352569/1‑141 (MQ=255)
                          tataATAATAGAGTCGCCTATCTCTCAGGCGTCGATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTT‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa                                                                                                                  >  2:280738/1‑140 (MQ=255)
                           ataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa                                                                                                                 >  2:493284/1‑139 (MQ=255)
                            taataaTAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaac                                                                                                                <  2:29742/141‑4 (MQ=255)
                            aaataatAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTT‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaac                                                                                                                <  1:99481/140‑4 (MQ=255)
                             aataatAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaaag                                                                                                               >  2:647690/1‑137 (MQ=255)
                             aataatAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACg                                                                                                               >  2:111394/1‑141 (MQ=255)
                               taatagAGCCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                             <  2:376500/138‑1 (MQ=255)
                               gaatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGGACATTAC‑T‑T‑T‑GCTAATC‑ATTTGCGTTCACATCATAGCACCAGTGATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTGGTAAACgga                                                                                                             >  2:96135/4‑139 (MQ=255)
                                agtagAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCa                                                                                                             <  1:206125/141‑1 (MQ=255)
                                aatagGGTCGCCTATATCTCAGGCGTCAATT‑‑GACGAACAGAGGCGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCCGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAATGCaa                                                                                                            <  1:469100/139‑1 (MQ=255)
                                 atagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaac                                                                                                           >  2:498300/2‑140 (MQ=255)
                                  tagAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAt                                                                                                           <  1:407826/141‑1 (MQ=255)
                                  tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGCGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca                                                                                                          <  1:292403/141‑3 (MQ=255)
                                  tagAGTCGCCTATCCCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAt                                                                                                           <  1:53886/141‑1 (MQ=255)
                                   agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                         >  2:571661/1‑138 (MQ=255)
                                   agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                         >  1:270264/1‑138 (MQ=255)
                                   agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                         >  2:297534/1‑138 (MQ=255)
                                   agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                         <  1:277141/141‑4 (MQ=255)
                                   agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑T‑T‑TGCGAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                         >  2:629138/1‑138 (MQ=255)
                                    gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                                                                                                        <  1:617180/141‑5 (MQ=255)
                                      gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACaa                                                                                                       <  2:400338/141‑1 (MQ=255)
                                      gTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaata                                                                                                      <  1:14081/141‑7 (MQ=255)
                                       tCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataa                                                                                                     <  1:618995/141‑8 (MQ=255)
                                       tCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataa                                                                                                     >  1:162660/1‑134 (MQ=255)
                                       tCGCCTATCTCCCAGGCCTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataa                                                                                                     <  1:8777/141‑8 (MQ=255)
                                        cGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataat                                                                                                    >  2:379385/1‑133 (MQ=255)
                                        cGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataat                                                                                                    >  1:261191/1‑133 (MQ=255)
                                        cGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGGGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataat                                                                                                    >  1:358919/1‑133 (MQ=255)
                                         gCCTATCTCTCAGGCGTCAATT‑‑GACGCGATGAGGGTGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaacaatt                                                                                                   <  2:300611/141‑10 (MQ=255)
                                         cccTATCTCTCGGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCAAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatt                                                                                                   <  2:59850/140‑10 (MQ=255)
                                          ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTTTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                  >  2:173791/1‑131 (MQ=255)
                                          ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                  >  1:81893/1‑131 (MQ=255)
                                          ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCACCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                  <  1:97113/141‑11 (MQ=255)
                                          ccTAGCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                  <  1:602673/141‑11 (MQ=255)
                                            tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                >  1:508557/1‑129 (MQ=255)
                                            tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTATTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                >  2:13627/1‑129 (MQ=255)
                                            tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                >  1:93114/1‑129 (MQ=255)
                                             ttctctcAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAT‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACGTCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                               <  1:450432/140‑14 (MQ=255)
                                             aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                               >  2:580444/1‑128 (MQ=255)
                                             aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                               >  1:168804/1‑128 (MQ=255)
                                             aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                               >  2:577827/1‑128 (MQ=255)
                                             aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑T‑GCTAATC‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                               >  1:568979/1‑128 (MQ=255)
                                                  tcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑AAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTCGACGCAATACAAAATAGGTTACag                                                                                           >  2:170845/1‑140 (MQ=255)
                                                      gCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAg                                                                                       >  2:526166/1‑141 (MQ=255)
                                                          cAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGc                                                                                   >  1:464158/1‑141 (MQ=255)
                                                           aaTTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCa                                                                                  <  2:454536/141‑1 (MQ=255)
                                                             tttGGACGCAGACAGGAGGTGTA‑TCA‑G‑G‑T‑GACGCTT‑ATTTTCGTTCACATCATAGCACCAGGCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCAcc                                                                                <  2:63656/141‑1 (MQ=255)
                                                                           ggaggTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCt                                                                  >  2:26504/1‑141 (MQ=255)
                                                                                    ttaA‑G‑G‑T‑GATGCGT‑CTTTTCGTTCACATCCTAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATCGGCTAAGTAGACGCAATACAAAATCGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCg                                                          <  1:86504/140‑1 (MQ=255)
                                                                                                aTGCTT‑ATTTTCGTTCACATCATAGCACCAGTGATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGt                                                  >  2:190265/1‑141 (MQ=255)
                                                                                                       aTTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGcccctcgagagggc                                            >  2:624889/1‑128 (MQ=255)
                                                                                                           tctgtcatatcataGCACCAGTCATCATTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTg                                        <  2:663060/137‑1 (MQ=255)
                                                                                                              ttCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGgtg                                     <  1:338440/141‑1 (MQ=255)
                                                                                                                   atcatAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTCAGTAGACGCAATACAAAATAGGTGACATTTAGCCGCACCAATAAGAATCCCCTCACTTCCGCAAATAGTGAGGGGGTTGGTGTATaa                                >  2:135692/1‑141 (MQ=255)
                                                                                                                               gTCACCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAACATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTAt                    <  1:133167/141‑1 (MQ=255)
                                                                                                                                      gTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGtt             <  2:652215/141‑1 (MQ=255)
                                                                                                                                      gTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGtt             <  2:352569/141‑1 (MQ=255)
                                                                                                                                          cTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCt         >  1:226948/1‑141 (MQ=255)
                                                                                                                                           tgtgCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCGGTCCCGGCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGGCtt        >  1:153638/1‑141 (MQ=255)
                                                                                                                                           tgtgCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCtt        >  2:615313/1‑141 (MQ=255)
                                                                                                                                                 aTTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATtat  <  1:358101/141‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                            
GACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑T‑GATGCTT‑ATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTAT  >  CP000730/1929779‑1930058

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A